1
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Possibility to Detect Reproducibly some 5-10 Å Conformational Differences
by Conventional Techniques: Physiologically Defined Lattice Transformations
in Bacteriophage T4. ACTA ACUST UNITED AC 2020. [DOI: 10.1017/s0424820100070163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
It was demonstrated that during maturation the proteins of the surface
lattice of a virus shell undergo conformational changes on the level of
quarternary structure. The conventional methods of negative stain and
information processing allow for detecting differences between two
conformational states of some 5 Å, although the information on the absolute
structure and its changes are estimated not to be better than 20-30 Å.
Attempts for refining the methods in view of demonstrating tertiary
structure changes of the subunits involved are discussed. The general
biological relevance of these studies are emphasized, particularly in view
of studying control mechanisms operating at the level of gene
products.
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2
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Shu D, Guo P. Only one pRNA hexamer but multiple copies of the DNA-packaging protein gp16 are needed for the motor to package bacterial virus phi29 genomic DNA. Virology 2003; 309:108-13. [PMID: 12726731 DOI: 10.1016/s0042-6822(03)00011-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A common feature in the maturation of linear dsDNA viruses is that the lengthy viral genome is translocated with remarkable velocity into a limited space within a preformed protein shell using ATP as motor energy. Most biomotors, such as myosin, kinesin, DNA-helicase, and RNA polymerase, contain one ATP-binding component that acts processively. An examination of the well-studied dsDNA viruses reveals that DNA packaging motors involve two nonstructural components. Which component of the motor is the integrated processive factor to turn the motor has not been identified. In bacterial virus phi 29, these two components consist of a gp16 protein and an RNA molecule called pRNA. We have previously predicted and recently confirmed that gp16 binds ATP. It is generally believed that gp16 serves as an ATP-binding and processive component to drive the motor. In this article, phi 29 DNA-packaging intermediates were purified in quantity and examined to differentiate the role between gp16 and pRNA. It was found that the pRNA hexamer is an integral motor component, while gp16 is not stably bound. Only one pRNA hexamer, but multiple copies of gp16, were needed to accomplish DNA packaging. pRNA functions continuously during the entire DNA translocation process, suggesting that pRNA is a vital part of the DNA packaging motor.
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Affiliation(s)
- Dan Shu
- Department of Pathobiology and Purdue Cancer Center, Purdue University, West Lafayette, IN 47907, USA
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3
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Lin H, Rao VB, Black LW. Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4. J Mol Biol 1999; 289:249-60. [PMID: 10366503 DOI: 10.1006/jmbi.1999.2781] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteriophage DNA packaging results from an ATP-driven translocation of concatemeric DNA into the prohead by the phage terminase complexed with the portal vertex dodecamer of the prohead. Functional domains of the bacteriophage T4 terminase and portal gene 20 product (gp20) were determined by mutant analysis and sequence localization within the structural genes. Interaction regions of the portal vertex and large terminase subunit (gp17) were determined by genetic (terminase-portal intergenic suppressor mutations), biochemical (column retention of gp17 and inhibition of in vitro DNA packaging by gp20 peptides), and immunological (co-immunoprecipitation of polymerized gp20 peptide and gp17) studies. The specificity of the interaction was tested by means of a phage T4 HOC (highly antigenicoutercapsid protein) display system in which wild-type, cs20, and scrambled portal peptide sequences were displayed on the HOC protein of phage T4. Binding affinities of these recombinant phages as determined by the retention of these phages by a His-tag immobilized gp17 column, and by co-immunoprecipitation with purified terminase supported the specific nature of the portal protein and terminase interaction sites. In further support of specificity, a gp20 peptide corresponding to a portion of the identified site inhibited packaging whereas the scrambled sequence peptide did not block DNA packaging in vitro. The portal interaction site is localized to 28 residues in the central portion of the linear sequence of gp20 (524 residues). As judged by two pairs of intergenic portal-terminase suppressor mutations, two separate regions of the terminase large subunit gp17 (central and COOH-terminal) interact through hydrophobic contacts at the portal site. Although the terminase apparently interacts with this gp20 portal peptide, polyclonal antibody against the portal peptide appears unable to access it in the native structure, suggesting intimate association of gp20 and gp17 possibly internalizes terminase regions within the portal in the packasome complex. Both similarities and differences are seen in comparison to analogous sites which have been identified in phages T3 and lambda.
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Affiliation(s)
- H Lin
- Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore, Baltimore, MD, 21201-1503, USA
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4
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Andreadis JD, Black LW. Substrate mutations that bypass a specific Cpn10 chaperonin requirement for protein folding. J Biol Chem 1998; 273:34075-86. [PMID: 9852065 DOI: 10.1074/jbc.273.51.34075] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacteriophage T4 GroES homologue, gp31, in conjunction with the Escherichia coli chaperonin GroEL, is both necessary and sufficient to fold the T4 major capsid protein, gp23, to a state competent for capsid assembly as shown by in vivo expression studies. GroES is unable to function in this role as a productive co-chaperonin. The sequencing and characterization of mutations within gp23 that confer GroEL and gp31 chaperonin-independent folding of the mutant protein suggest that the chaperonin requirements are due to specific sequence determinants or structures in critical regions of gp23 that behave in an additive fashion to confer a chaperonin bypass phenotype. Conservative amino acid substitutions in these critical regions enable gp23 to fold in a GroEL-gp31 chaperonin-independent mode, albeit less efficiently than wild type, both in vivo and in vitro. Although the presence of functional GroEL-gp31 enhances folding of the mutated gp23 in vivo, GroEL-GroES has no such effect. Site-directed mutagenesis experiments suggest that a translational pausing mechanism is not responsible for the bypass mutant phenotype. Polyhead reassembly experiments are also consistent with direct, post-translational effects of the bypass mutations on polypeptide folding. Given our finding that gp31 is not required for the binding of the major capsid protein to GroEL and that active GroES is incapable of folding the gp23 polypeptide chain to native conformation, our results suggest co-chaperonin specificity in the folding of certain substrates.
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Affiliation(s)
- J D Andreadis
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland 21201, USA
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5
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Jardine PJ, McCormick MC, Lutze-Wallace C, Coombs DH. The bacteriophage T4 DNA packaging apparatus targets the unexpanded prohead. J Mol Biol 1998; 284:647-59. [PMID: 9826505 DOI: 10.1006/jmbi.1998.2178] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During the morphogenesis of the bacteriophage T4 capsid, a conformational change of the major head shell protein, gene product (gp) 23, causes a 50% increase in capsid volume. This expansion is required to accept the full length chromosome and, therefore, must precede the completion of packaging. The expanded shell is thinner and more stable than its precursor, and can bind accessory proteins which further stabilize it. In phages lambda, T3, T7 and P22, expansion occurs during DNA packaging. However, in T4, expanded capsids can package DNA in vitro and expansion occurs in cells infected with packaging-defective mutants, raising the possibility that expansion and packaging are not coupled. Proteolytically mature gp23 (gp23*) in unexpanded proheads is sensitive to chymotrypsin cleavage at Phe154-Ser155, creating a 38 kDa peptide, while gp23* in expanded capsids is refractory to the protease. We used an expansion assay based on this protease sensitivity to determine the expansion status of capsids isolated from various packaging-defective mutants with the goal of determining whether packaging and expansion are normally linked. In infections at 20 degrees C, mutants in the packaging enzymes gp16 and gp17 fail to expand. However, in gene 49(-) mutants, which initiate packaging but fail to complete it, expansion is complete. Thus, packaging drives expansion, and the unexpanded prohead is the substrate for the packaging reaction. We also show that expansion observed in 16(-) and 17(-) infections at 37 degrees C is linked to aberrant packaging. Capsids produced at 15 minutes, when no packaging can be detected, never expand. However, by 35 minutes when aberrant packaging begins, so does expansion of freshly made capsids. Thus in all cases now examined, expansion is only observed in vivo when DNA packaging is also occurring, indicating that these two processes are coupled.
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Affiliation(s)
- P J Jardine
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, E3B 6E1, Canada
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6
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Franklin JL, Haseltine D, Davenport L, Mosig G. The largest (70 kDa) product of the bacteriophage T4 DNA terminase gene 17 binds to single-stranded DNA segments and digests them towards junctions with double-stranded DNA. J Mol Biol 1998; 277:541-57. [PMID: 9533879 DOI: 10.1006/jmbi.1998.1619] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteriophage terminases are oligomeric multifunctional proteins that bind to vegetative DNA, cut it and, together with portal proteins, translocate the DNA into preformed heads. Most terminases are encoded by two partially overlapping genes. In phage T4 they are genes 16 and 17. We have shown before that the larger of these, gene 17, can yield, in addition to a full-length 70 kDa product, several shorter peptides. At least two of these, gene product (gp) 17' and gp17", are initiated in the same reading frame as the 70 kDa gp17 from internal ribosome binding sites. Most of the shorter gp17 s contain predicted ATPase motifs, but only the largest (70 kDa) peptide has a predicted single-stranded DNA binding domain. Here we describe the DNA binding and cutting properties of the purified 70 kDa protein, expressed from two different clones containing gene 17 but no other T4 gene. Epitope-specific antibodies, which recognize several different gene 17 products in extracts of induced clones or of T4-infected cells, precipitate the purified 70 kDa gp17. When Mg2+ is chelated by EDTA this 70 kDa protein binds to single-stranded DNA, preferentially to junctions of single- and double-stranded DNA segments. It does not bind to blunt-ended double-stranded DNA. When Mg2+ is present the purified 70 kDa gp17 digests single-stranded segments preferentially up to junctions with double-stranded DNA. A 70 kDa gp17 from a P379L temperature sensitive (ts) mutant, which has lost the nuclease and ATPase activities, retains the single-stranded DNA binding activity. Taken together with earlier findings these results support a model for packaging of T4 DNA from single-stranded regions in recombinational or replicative intermediates, which occur at nearly random positions of the genome. This mechanism may be an alternative to site-specific initiation of packaging proposed by other investigators.
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Affiliation(s)
- J L Franklin
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235, USA
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7
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Franklin JL, Mosig G. Expression of the bacteriophage T4 DNA terminase genes 16 and 17 yields multiple proteins. Gene X 1996; 177:179-89. [PMID: 8921865 DOI: 10.1016/0378-1119(96)00299-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The products of the bacteriophage T4 terminase genes 16 and 17 are known to mediate cutting and packaging of concatemeric vegetative DNA. We show here that the larger of these genes, 17, yields multiple protein species. The complex expression of the T4 terminase genes includes overlapping transcripts, probably initiated from multiple promoters, RNA processing at certain preferred sites and translation initiation from multiple ribosome binding sites (RBS). Translation initiation from these RBS may be modulated by inverted repeat (IR) sequences whose folding can be predicted to differ in different RNA species. In T4 infected bacteria, genes 16 and 17 are probably co-transcribed from several near-consensus late promoters upstream from gene 16, and processed at multiple sites. Additional 5' ends of late transcripts are located downstream from a near-consensus late promoter inside gene 17 and further downstream, unrelated to any known promoter consensus sequence. The gene 17 transcripts that are initiated or cleaved internally contain RBS for shorter open reading frames (ORFs) in the same frame as full-length gene product (gp) 17 of 70 kDa. The truncated proteins, a 59-kDa gp17' and a 45-kDa gp17", are synthesized from cloned gene 17 segments in which the first gene 17 RBS is deleted. Expression of gene 17 is different in BL21(DE3) or W3110[pACT7] host bacteria. The gp17' and gp17" proteins are predicted to contain one or more of the ATPase motifs that are common among large subunits of other phage terminases. They lack a predicted single stranded (ss) DNA binding motif that is unique the large terminase proteins in T4 gp17, and that has been implicated in recognizing ssDNA regions in replicating and recombining T4DNA destined to be packaged. We hypothesize that a truncated gene 17' is an evolutionary precursor of the full-size T4 gene 17. Its function may have been maintained to allow processive packaging from double stranded (ds) DNA ends.
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Affiliation(s)
- J L Franklin
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235, USA
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8
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Black LW. DNA packaging and cutting by phage terminases: control in phage T4 by a synaptic mechanism. Bioessays 1995; 17:1025-30. [PMID: 8634063 DOI: 10.1002/bies.950171206] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phage DNA packaging occurs by DNA translocation into a prohead. Terminases are enzymes which initiate DNA packaging by cutting the DNA concatemer, and they are closely fitted structurally to the portal vertex of the prohead to form a 'packasome'. Analysis among a number of phages supports an active role of the terminases in coupling ATP hydrolysis to DNA translocation through the portal. In phage T4 the small terminase subunit promotes a sequence-specific terminase gene amplification within the chromosome. This link between recombination and packaging suggests a DNA synapsis mechanism by the terminase to control packaging initiation, formally homologous to eukaryotic chromosome segregation.
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Affiliation(s)
- L W Black
- Department of Biological Chemistry, University of Maryland Medical School, Baltimore 21201, USA
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9
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Kellenberger E, Wunderli-Allenspach H. Electron microscopic studies on intracellular phage development--history and perspectives. Micron 1995; 26:213-45. [PMID: 7788280 DOI: 10.1016/0968-4328(94)00051-q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review is centered on the applications of thin sections to the study of intracellular precursors of bacteriophage heads. Results obtained with other preparation methods are included in so far as they are essential for the comprehension of the biological problems. This type of work was pioneered with phage T4, which contributed much to today's understanding of morphogenesis and form determination. The T4 story is rich in successes, but also in many fallacies. Due to its large size, T4 is obviously prone to preparation artefacts such as emptying, flattening and others. Many of these artefacts were first encountered in T4. Artefacts are mostly found in lysates, however, experience shows that they are not completely absent from thin sections. This can be explained by the fact that permeability changes induced by fixatives occur. The information gained from T4 was profitably used for the study of other phages. They are included in this review as far as electron microscopic studies played a major role in the elucidation of their morphogenetic pathways. Research on phage assembly pathways and form determination is a beautiful illustration for the power of the integrated approach which combines electron microscopy with biochemistry, genetics and biophysics. As a consequence, we did not restrict ourselves to the review of electron microscopic work but tried to integrate pertinent data which contribute to the understanding of the molecular mechanisms acting in determining the form of supramolecular structures.
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Affiliation(s)
- E Kellenberger
- Department of Microbiology, Biocenter of the University, Basel, Switzerland
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10
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Defives C, Werquin M, Hornez JP, Derieux JC. In vivo morphogenesis and growth characteristics of phages CM (Myoviridae) virulent forRhizobium meliloti. Curr Microbiol 1993. [DOI: 10.1007/bf01575997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Steven AC, Greenstone HL, Booy FP, Black LW, Ross PD. Conformational changes of a viral capsid protein. Thermodynamic rationale for proteolytic regulation of bacteriophage T4 capsid expansion, co-operativity, and super-stabilization by soc binding. J Mol Biol 1992; 228:870-84. [PMID: 1469720 DOI: 10.1016/0022-2836(92)90871-g] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have used differential scanning calorimetry in conjunction with cryo-electron microscopy to investigate the conformational transitions undergone by the maturing capsid of phage T4. Its precursor shell is composed primarily of gp23 (521 residues): cleavage of gp23 to gp23* (residues 66 to 521) facilitates a concerted conformational change in which the particle expands substantially, and is greatly stabilized. We have now characterized the intermediate states of capsid maturation; namely, the cleaved/unexpanded, state, which denatures at tm = 60 degrees C, and the uncleaved/expanded state, for which tm = 70 degrees C. When compared with the precursor uncleaved/unexpanded state (tm = 65 degrees C), and the mature cleaved/expanded state (tm = 83 degrees C, if complete cleavage precedes expansion), it follows that expansion of the cleaved precursor (delta tm approximately +23 degrees C) is the major stabilizing event in capsid maturation. These observations also suggest an advantage conferred by capsid protein cleavage (some other phage capsids expand without cleavage): if the gp23-delta domains (residues 1 to 65) are not removed by proteolysis, they impede formation of the stablest possible bonding arrangement when expansion occurs, most likely by becoming trapped at the interface between neighboring subunits or capsomers. Icosahedral capsids denature at essentially the same temperatures as tubular polymorphic variants (polyheads) for the same state of the surface lattice. However, the thermal transitions of capsids are considerably sharper, i.e. more co-operative, than those of polyheads, which we attribute to capsids being closed, not open-ended. In both cases, binding of the accessory protein soc around the threefold sites on the outer surface of the expanded surface lattice results in a substantial further stabilization (delta tm = +5 degrees C). The interfaces between capsomers appear to be relatively weak points that are reinforced by clamp-like binding of soc. These results imply that the "triplex" proteins of other viruses (their structural counterparts of soc) are likely also to be involved in capsid stabilization. Cryo-electron microscopy was used to make conclusive interpretations of endotherms in terms of denaturation events. These data also revealed that the cleaved/unexpanded capsid has an angular polyhedral morphology and has a pronounced relief on its outer surface. Moreover, it is 14% smaller in linear dimensions than the cleaved/expanded capsid, and its shell is commensurately thicker.
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Affiliation(s)
- A C Steven
- Laboratory of Structural Biology, National Institute of Arthritis Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
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12
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Kellenberger E, Johansen R, Maeder M, Bohrmann B, Stauffer E, Villiger W. Artefacts and morphological changes during chemical fixation. J Microsc 1992; 168:181-201. [PMID: 1464902 DOI: 10.1111/j.1365-2818.1992.tb03260.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The normally 'condensed' (darkly stained) chromosomes of dinoflagellates decondense by swelling. This occurs in an increasing number of cells when the concentration of added OsO4 is decreased. With different fixatives other types of disintegration can be observed, which vary with the concentration. With cryofixation and freeze-substitution the chromosomes are most 'condensed'. Escherichia coli infected with bacteriophage T4, with or without active lysozyme production, were studied by optical densitometry for partial lysis and by light and electron microscopy for observing swelling. When active lysozyme is present some of the acrolein (2.5%)-glutaraldehyde (2%)-fixed cells swell at 0 degrees C, but do not in the absence of lysozyme nor when fixed at room temperature. If OsO4 is added at concentrations < or = 0.5%, partial lysis occurs when lysozyme is present. The optical density decreases, the cells lose some matter and swell slightly. The corresponding electron micrographs show gap formation by curdling and/or a decreased concentration of the cytoplasm which reveals certain phage-related particles.
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13
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Müller M, Wurtz M, Kellenberger E, Aebi U. Physiological, morphological, and physicochemical characterization of a novel Escherichia coli bacteriophage, phage MM. J Struct Biol 1991; 106:17-30. [PMID: 2059549 DOI: 10.1016/1047-8477(91)90059-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A double-stranded DNA containing, T even-like, Escherichia coli bacteriophage, called MM, has been isolated from the local sewage and purified by polyethylene glycol precipitation followed by banding on a cesium chloride three-step gradient. It yields a burst size of 75 particles per infected cell, and has an adsorption coefficient of 3.3 x 10(-10) cm3/min and a latent period of 45 min. Electron microscopy of phage MM reveals an isometric icosahedral head, 92 nm long and 81 nm wide, and a 112-nm-long contractile tail with six pairs of 40-nm-long fibers attached to its baseplate. Phage MM appears similar to E. coli phage T4 or Salmonella phage O1. The density of phage MM in cesium chloride is 1.515 g/ml, and its total mass is 144 MDa. Gel electrophoresis of purified MM capsids displays two major capsid proteins in approximately equimolar amounts and with apparent molecular masses of 38 and 15 kDa. Similarly, purified MM tails yield two major polypeptides with apparent molecular masses of 55 and 16 kDa, most likely representing the major tail sheath and tail tube polypeptides. Its double-stranded DNA has a G-C content of 50%, a length of 131 kilobases (kb), and a mass of 89 MDa.
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Affiliation(s)
- M Müller
- M. E. Müller-Institute for High-Resolution Electron Microscopy, Biocenter, University of Basel, Switzerland
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14
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Abstract
The shape of the DNA-containing heads of many bacteriophages is not only determined by the properties of the protein subunits which build the shell (capsid) but also by the scaffolding core which is a transient structure of the prohead. The form-determining properties of the scaffolding proteins have been characterized by genetic methods based on conditional mutants and site-directed mutagenesis. The mechanism of form determination has been studied by in vitro assembly experiments. The theoretical background is discussed and different models for mechanisms of form determination are considered. Definitive decisions about the validity of a model is still limited by the difficulty of obtaining unambiguous answers on the stoichiometry and the fine structure of the scaffold because of their high instability.
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Affiliation(s)
- E Kellenberger
- Department of Microbiology, University of Basel, Switzerland
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15
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Baschong W, Aebi U, Baschong-Prescianotto C, Dubochet J, Landmann L, Kellenberger E, Wurtz M. Head structure of bacteriophages T2 and T4. JOURNAL OF ULTRASTRUCTURE AND MOLECULAR STRUCTURE RESEARCH 1988; 99:189-202. [PMID: 3198952 DOI: 10.1016/0889-1605(88)90063-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The length-to-width ratios of bacteriophage T2 and T4 heads and stereometric angles specifying the prolate icosahedral T2 capsid were evaluated on electron micrographs recorded from samples prepared by a variety of methods. The copy numbers of the major capsid protein, gp23*, of T2 and T4 phages were compared by quantitative gel electrophoresis. Taken together, the resulting values are most compatible with triangulation numbers T = 13 and Q = 21 for both T2 and T4, thus confirming the previously proposed capsid architecture of T4 revealed by indirect measurements and thereby eliminating the repeatedly reported discrepancy between T2 and T4 in favor of a common Q number of 21 corresponding to 960 copies of gp23*.
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Affiliation(s)
- W Baschong
- M. E. Müller-Institute for High Resolution Electron Microscopy at the Biocenter, University of Basel, Switzerland
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16
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Rao VB, Black LW. Cloning, overexpression and purification of the terminase proteins gp16 and gp17 of bacteriophage T4. Construction of a defined in-vitro DNA packaging system using purified terminase proteins. J Mol Biol 1988; 200:475-88. [PMID: 3294420 DOI: 10.1016/0022-2836(88)90537-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Terminases of double-stranded DNA bacteriophages are required for packaging and generation of terminii in replicated concatemeric DNA molecules. Genetic evidence suggests that these functions in phage T4 are carried out by the products of genes 16 and 17. We cloned these T4 genes into a heat-inducible cI repressor-lambda PL promoter vector system, and overexpressed them in Escherichia coli. We developed an in-vitro DNA packaging system, which, consistent with the genetic data, shows an absolute requirement for the terminase proteins. The overexpressed terminase proteins gp16 and gp17 appear to form a specific complex and an ATP binding site is present in the gp17 molecule. We purified the terminase proteins either as individual gp16 or gp17 proteins, or as a gp16-gp17 complex. The gp16 function of the terminase complex is dispensable for packaging mature DNA, whereas gp17 is essential for packaging DNA under any condition tested. We constructed a defined in-vitro DNA packaging system with the purified terminase proteins, purified proheads and a DNA-free phage completion gene products extract. All the components of this system can be stored at -90 degrees C without loss of packaging activity. The terminase proteins, therefore, may serve as useful reagents for mechanistic studies on DNA packaging, as well as to develop T4 as a packaging-cloning vector.
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Affiliation(s)
- V B Rao
- Department of Biological Chemistry, University of Maryland Medical School, Baltimore 21201
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17
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Wu DG, Black LW. Gene amplification mechanism for the hyperproduction of T4 bacteriophage gene 17 and 18 proteins. J Mol Biol 1987; 195:769-83. [PMID: 3498845 DOI: 10.1016/0022-2836(87)90483-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacteriophage T4 mutants hyperproducing gene 17 protein (Hp17) have been isolated at high frequency by growing gene 17 amber mutants on ochre suppressor strains of Escherichia coli. Most mutants showed the co-hyperproduction of gene 18 protein, although one anomalous mutant hyperproduced a 60,000 Mr partial polypeptide of gene 18. Hybridization of T4 late RNAs to cloned plasmid DNA containing genes 17, 18 or control T4 genes revealed that approximately five times more gene 17 mRNA and two to three times more gene 18 mRNA were synthesized in the Hp17 mutant infections. DNA-DNA hybridizations showed that Hp17 mutant DNA contained two to three times more copies of genes 17 and 18 than wild-type DNA. Southern blot analysis suggested that Hp17 mutants carry a direct tandem repeat of the gene 17-18 region, with variable copy number from one to at least six copies. Hyperproduction of gene 17 and 18 proteins appears therefore to result from gene amplification specific to the gene 17-18 region. In contrast to gene duplications reported in lambda and T4 phage, and numerous cases of gene amplification in bacteria, a similar or identical novel junctional fragment created by the amplification event was observed among 28 independent T4 Hp17 isolates; therefore, the mechanism giving gise to amplified sequences may involve specific sequences in this region of the T4 genome.
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Affiliation(s)
- D G Wu
- Department of Biological Chemistry, University of Maryland School of Medicine, Baltimore 21201
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18
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Contrast Formation in Electron Microscopy of Biological Material. ADVANCES IN ELECTRONICS AND ELECTRON PHYSICS 1985. [DOI: 10.1016/s0065-2539(08)60354-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Abstract
T4 DNA structural requirements for encapsidation in vivo were investigated, using thin-section electron microscopy to quantitate the kinetics and yields of head intermediates after synchronous DNA packaging into accumulated processed proheads. UV irradiation (254 nm) of T4-infected bacteria just before initiation of encapsidation resulted in a reduction in the rate of DNA packaged measured by electron microscopy and in the yield of viable phage progeny. In UV-irradiated infections with excision-deficient mutants (denV-), the extent of packaging decline was proportional to the UV dose and phage yields were lower than expected based on the packaging levels observed by microscopy. Rescue analysis of progeny from such infections revealed elevated levels of nonviable virions. Pyrimidine dimers were encapsidated in denV- infections, but in excision-competent infections (denV+) dimers were not packaged. A UV-independent, 15 to 20% packaging arrest was also observed when denV endonuclease was inactive during encapsidation, indicating a denV requirement to achieve normal T4 packaging levels. Pyrimidine dimers apparently represent or induce transient blockage of DNA encapsidation or both, causing a decline in the rate. This is in contrast to other DNA structural blocks to packaging induced by mutations in T4 genes 30 and 49, which appear to arrest the process.
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Völker TA, Kuhn A, Showe MK, Bickle TA. Gene 67, a new, essential bacteriophage T4 head gene codes for a prehead core component, PIP. II. The construction in vitro of unconditionally lethal mutants and their maintenance. J Mol Biol 1982; 161:491-504. [PMID: 7154088 DOI: 10.1016/0022-2836(82)90403-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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21
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Kuhn AH, Moncany ML, Kellenberger E, Hausmann R. Involvement of the bacterial groM gene product in bacteriophage T7 reproduction. I. Arrest at the level of DNA packaging. J Virol 1982; 41:657-73. [PMID: 6281476 PMCID: PMC256795 DOI: 10.1128/jvi.41.2.657-673.1982] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The multiplication of bacteriophage T7 is blocked in Escherichia coli M. The genetic determinant of this ability (groM) to inhibit T7 growth was transferred to an E. coli K-12 recipient by means of conjugation. We determined at which precise step T7 maturation is blocked. Phage-directed protein and DNA synthesis as well as degradation of host DNA were not qualitatively affected. Instead of infective phages, only preheads were produced. These, however, were maturable in vitro. The newly synthesized phage DNA accumulated in a concatemeric form and matured from its tetrameric or longer forms (very fast sedimenting DNA) only into its dimeric form (fast-sedimenting DNA) or longer forms. The following step, i.e., the maturation of the dimeric to unit-length DNA, was not observed. Since the concatemeric form of T7 DNA accumulated in spite of the presence of maturable preheads, it is likely that the maturation process was blocked at the level of DNA packaging. As intermediates in the packaging process, we found some prehead-DNA complexes. We interpreted these as true assembly intermediates (or breakdown products thereof), since the attached DNA was still in its concatemeric form. This shows that the very first DNA packaging step, the binding of the progeny DNA to the preheads, was obviously not blocked. Rather, a later step, such as the filling of the preheads with T7 DNA or the stabilization of completely packaged particles (i.e., the final cutting of the concatemers into unit-size length), was inhibited.
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23
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24
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25
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Schaerli C. Head maturation pathway of bacteriophages T4 and T2. V. Maturable epsilon-particle accumulating an acridine-treated bacteriophage T4-infected cells. J Virol 1980; 33:830-44. [PMID: 6997509 PMCID: PMC288609 DOI: 10.1128/jvi.33.2.830-844.1980] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A maturable head-related particle of bacteriophage T4 has been identified and characterized. This epsilon-particle has the same size as the prehead, but its shell is made of the cleaved product of gene 23 (gp23*). It contains internal matter, most likely the processed core proteins, which is lost or modified by experimental manipulations. It accumulates, together with partially filled ("grizzled") heads, in T4 infected cells that are treated with 9-aminoacridine. On sections of "well-preserved" cells the epsilon-particles are not identifiable with certainty; a more or less empty breakdown product of them becomes visible when cytoplasmic leakage is induced. The number of particles per cell is then in agreement with the biochemically and with the number of particles counted in lysates. Morphologically and biochemically, the isolated epsilon-particles closely resemble the empty small particles of 17- -infected cells described in previous papers of this series. Both are composed of gp23* and are still unexpanded, so that they are not yet able to bind the minor head proteins soc and hoc. We discuss the possibility of the epsilon-particle being an intermediate on the normal T4 wild-type head maturation pathway.
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28
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Wunderli H, Couture E, Vince DA, Kellenberger E. Studies related to the head-maturation pathway of bacteriophages T4 And T2:II. nuclear disruption, protein synthesis and particle formation with the mutant 43-.30-.46-. JOURNAL OF SUPRAMOLECULAR STRUCTURE 1977; 7:163-90. [PMID: 599934 DOI: 10.1002/jss.400070203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We describe the aberrant phage multiplication of the triple conditional lethal mutant 43-(polymerase).30-(ligase).46-(exonuclease) of bacteriophage T4D in which phage DNA replication is arrested but some late protein synthesis occurs (33). The nuclear disruption is indistinguishable from wild type. Forty-five empty small and empty large particles are assembled per cell when the multiplicity of infection (m.o.i.) is 100. This number corresponds closely to the 38 phage equivalents of cleaved major head protein determined biochemically. By reducing the m.o.i. the number of observable particles decreases, reaching 1-5 per cell at an m.o.i. of 5(+5). The total synthesis of phage related proteins is not significantly dependant on the m.o.i. The synthesis of late proteins is about 10% of that of wild type at high m.o.i. and decreases with the m.o.i. The different early and late proteins do not show the same relative proportions as in wild type and respond differently to an increased m.o.i. These and other results are discussed with respect to the role of phage DNA in prehead assembly and head maturation.
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