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LaBianca K, Butura J, McKnight A, Pan K, Whelan S, Punska E, Pause R, Igbinosa B, Ribbe A, Chien P, Russell D, Garlena R, Hatfull G, Jacobs-Sera D, Rocheleau J. Complete genome sequence of phi29-like Microbacterium foliorum podovirus phage PineapplePizza. Microbiol Resour Announc 2023; 12:e0047823. [PMID: 37671874 PMCID: PMC10586137 DOI: 10.1128/mra.00478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/16/2023] [Indexed: 09/07/2023] Open
Abstract
Bacteriophage PineapplePizza is a podovirus infecting Microbacterium foliorum NRRL B-24224. The genome is 16,662 bp long and contains 23 predicted protein-coding genes. Interestingly, PineapplePizza shows amino acid similarities to well-studied Bacillus subtilis phage phi29.
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Affiliation(s)
- Kylie LaBianca
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jessica Butura
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Arden McKnight
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Karin Pan
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Sean Whelan
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Elizabeth Punska
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Robert Pause
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Bright Igbinosa
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Alexander Ribbe
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Daniel Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rebecca Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jessica Rocheleau
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
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2
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Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S. Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor. Biochemistry 2021; 60:886-897. [PMID: 33689296 DOI: 10.1021/acs.biochem.0c00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage ϕ29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete ϕ29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage ϕ29 and suggested how the individual domains of gp16 work together to power such translocation.
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Affiliation(s)
- Abdullah F U H Saeed
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
| | - Chun Chan
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hongxin Guan
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bing Gong
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535000, China
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for RNA Nanobiotechnology and Nanomedicine, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaolin Cheng
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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3
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A Novel Genus of Actinobacterial Tectiviridae. Viruses 2019; 11:v11121134. [PMID: 31817897 PMCID: PMC6950372 DOI: 10.3390/v11121134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomycesphages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcusphage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.
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4
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Chung CH, Walter MH, Yang L, Chen SCG, Winston V, Thomas MA. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics 2017; 18:350. [PMID: 28472946 PMCID: PMC5418689 DOI: 10.1186/s12864-017-3744-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Most tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends. Result We sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of ‘neighboring coverage ratios’ and ‘read edge frequencies’ from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences. Conclusions The Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3744-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng-Han Chung
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA.
| | - Michael H Walter
- Department of Biology, University of Northern Iowa, 144 McCollum Science Hall, Cedar Falls, IA, 50614-0421, USA
| | - Luobin Yang
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Shu-Chuan Grace Chen
- Department of Mathematics and Statistics, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8085, USA
| | - Vern Winston
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
| | - Michael A Thomas
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Pocatello, ID, 83209-8007, USA
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5
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Abstract
During the course of evolution, viruses have learned to take advantage of the natural resources of their hosts for their own benefit. Due to their small dimension and limited size of genomes, bacteriophages have optimized the exploitation of bacterial host factors to increase the efficiency of DNA replication and hence to produce vast progeny. The Bacillus subtilis phage φ29 genome consists of a linear double-stranded DNA molecule that is duplicated by means of a protein-primed mode of DNA replication. Its genome has been shown to be topologically constrained at the size of the bacterial nucleoid and, as to avoid generation of positive supercoiling ahead of the replication forks, the bacterial DNA gyrase is used by the phage. In addition, the B. subtilis actin-like MreB cytoskeleton plays a crucial role in the organization of φ29 DNA replication machinery in peripheral helix-like structures. Thus, in the absence of an intact MreB cytoskeleton, φ29 DNA replication is severely impaired. Importantly, MreB interacts directly with the phage membrane protein p16.7, responsible for attaching φ29 DNA at the cell membrane. Moreover, the φ29-encoded protein p56 inhibits host uracil-DNA glycosylase activity and has been proposed to be a defense mechanism developed by the phage to prevent the action of the base excision repair pathway if uracil residues arise in replicative intermediates. All of them constitute incoming examples on how viruses have profited from the cellular machinery of their hosts.
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6
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The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J Virol 2013; 87:8388-98. [PMID: 23698307 DOI: 10.1128/jvi.00831-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase. Such NTPases have been characterized in detail from both RNA and tailed DNA viruses. We present four crystal structures and the biochemical activity of a thermophilic NTPase, B204, from the nontailed, membrane-containing, hyperthermoacidophilic archaeal dsDNA virus Sulfolobus turreted icosahedral virus 2. These are the first structures of a genome-packaging NTPase from a nontailed, dsDNA virus with an archaeal host. The four structures highlight the catalytic cycle of B204, pinpointing the molecular movement between substrate-bound (open) and empty (closed) active sites. The protein is shown to bind both single-stranded and double-stranded nucleic acids and to have an optimum activity at 80°C and pH 4.5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism.
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7
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Levings CS, Sederoff RR. Nucleotide sequence of the S-2 mitochondrial DNA from the S cytoplasm of maize. Proc Natl Acad Sci U S A 2010; 80:4055-9. [PMID: 16593334 PMCID: PMC394199 DOI: 10.1073/pnas.80.13.4055] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondria from the S male-sterile cytoplasm (cms-S) of maize contain two plasmid-like DNAs, S-1 and S-2, that appear to be prominently involved with the cytoplasmic male sterility trait. The complete nucleotide sequence of the S-2 DNA molecule was determined by the chain termination method. The linear S-2 DNA molecule contains 5,452 base pairs and is terminated by exact 208-base-pair inverted repetitions. Two large open reading frames were identified in the S-2 DNA, suggesting the possibility of protein-encoding genes. The nucleotide sequence of the S-2 termini are discussed with regard to models proposed for the replication of linear DNA molecules.
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Affiliation(s)
- C S Levings
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27650
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8
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Casjens SR, Gilcrease EB. Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 2009; 502:91-111. [PMID: 19082553 DOI: 10.1007/978-1-60327-565-1_7] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Tailed-bacteriophage virions contain a single linear dsDNA chromosome which can range in size from about 18 to 500 kbp across the known tailed-phage types. These linear chromosomes can have one of several known types of termini as follows: cohesive ends (5'- or 3'-single-strand extensions), circularly permuted direct terminal repeats, short or long exact direct terminal repeats, terminal host DNA sequences, or covalently bound terminal proteins. These different types of ends reflect differing DNA replication strategies and especially differing terminase actions during DNA packaging. In general, complete genome sequence determination does not by itself elucidate the nature of these ends, so directed experimental analysis is usually required to understand the nature of the virion chromosome ends. This chapter discusses these methods.
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Affiliation(s)
- Sherwood R Casjens
- Division of Cell Biology and Immunology, Department of Pathology, University of Utah Medical School, Salt Lake City, UT, USA
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9
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Liao W, Song S, Sun F, Jia Y, Zeng W, Pang Y. Isolation, characterization and genome sequencing of phage MZTP02 from Bacillus thuringiensis MZ1. Arch Virol 2008; 153:1855-65. [DOI: 10.1007/s00705-008-0201-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 09/01/2008] [Indexed: 10/21/2022]
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10
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Grayson P, Molineux IJ. Is phage DNA 'injected' into cells--biologists and physicists can agree. Curr Opin Microbiol 2007; 10:401-9. [PMID: 17714979 PMCID: PMC2064038 DOI: 10.1016/j.mib.2007.04.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 04/17/2007] [Indexed: 12/31/2022]
Abstract
The double-stranded DNA inside bacteriophages is packaged at a density of approximately 500 mg/ml and exerts an osmotic pressure of tens of atmospheres. This pressure is commonly assumed to cause genome ejection during infection. Indeed, by the addition of their natural receptors, some phages can be induced in vitro to completely expel their genome from the virion. However, the osmotic pressure of the bacterial cytoplasm exerts an opposing force, making it impossible for the pressure of packaged DNA to cause complete genome ejection in vivo. Various processes for complete genome ejection are discussed, but we focus on a novel proposal suggesting that the osmotic gradient between the extracellular environment and the cytoplasm results in fluid flow through the phage virion at the initiation of infection. The phage genome is thereby sucked into the cell by hydrodynamic drag.
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Affiliation(s)
- Paul Grayson
- Department of Physics, California Institute of Technology, Pasadena, CA 91125
| | - Ian J. Molineux
- Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
- * Corresponding author. Phone: 512–471–3143
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11
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Moll WD, Guo P. Translocation of nicked but not gapped DNA by the packaging motor of bacteriophage phi29. J Mol Biol 2005; 351:100-7. [PMID: 16002084 DOI: 10.1016/j.jmb.2005.05.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 05/12/2005] [Accepted: 05/18/2005] [Indexed: 11/19/2022]
Abstract
The biomolecular mechanism that the double-stranded DNA viruses employ to insert and package their genomic DNA into a preformed procapsid is still elusive. To better characterize this process, we investigated packaging of bacteriophage phi29 DNA with structural alterations. phi29 DNA was modified in vitro by nicking at random sites with DNase I, or at specific sites with nicking enzyme N.BbvC IA. Single-strand gaps were created by expanding site-specific nicks with T4 DNA polymerase. Packaging of modified phi29 DNA was studied in a completely defined in vitro system. Nicked DNA was packaged at full genome length and with the same efficiency as untreated DNA. Nicks were not repaired during packaging. Gapped DNA was packaged only as a fragment corresponding to the DNA between the genome terminus and gap. Thus the phi29 DNA packaging machinery tolerated nicks, but stopped at gaps. The packaging motor did not require a nick-free DNA backbone, but the presence of both DNA strands, for uninterrupted packaging.
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Affiliation(s)
- Wulf-Dieter Moll
- Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
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12
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Strömsten NJ, Bamford DH, Bamford JKH. In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses. J Mol Biol 2005; 348:617-29. [PMID: 15826659 DOI: 10.1016/j.jmb.2005.03.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 03/01/2005] [Accepted: 03/01/2005] [Indexed: 10/25/2022]
Abstract
PRD1 is the type virus of the Tectiviridae family. Its linear double-stranded DNA genome has covalently attached terminal proteins and is surrounded by a membrane, which is further enclosed within an icosahedral protein capsid. Similar to tailed bacteriophages, PRD1 packages its DNA into a preformed procapsid. The PRD1 putative packaging ATPase P9 is a structural protein located at a unique vertex of the capsid. An in vitro system for packaging DNA into preformed empty procapsids was developed. The system uses cell extracts of overexpressed P9 protein and empty procapsids from a P9-deficient mutant virus infection and PRD1 DNA containing a LacZalpha-insert. The in vitro packaged virions produce distinctly blue plaques when plated on a suitable host. This is the first time that a viral genome is packaged in vitro into a membrane vesicle. Comparison of PRD1 P9 with putative packaging ATPase sequences from bacterial, archaeal and eukaryotic viruses revealed a new packaging ATPase-specific motif. Surprisingly the viruses having this packaging ATPase motif, and thus considered to be related, were the same as those recently grouped together using the coat protein fold and virion architecture. Our finding here strongly supports the idea that all these viruses infecting hosts in all domains of life had a common ancestor.
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Affiliation(s)
- Nelli J Strömsten
- Department of Biological and Environmental Sciences and Institute of Biotechnology, Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014, University of Helsinki, Helsinki, Finland
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13
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Vybiral D, Takác M, Loessner M, Witte A, von Ahsen U, Bläsi U. Complete nucleotide sequence and molecular characterization of two lytic Staphylococcus aureus phages: 44AHJD and P68. FEMS Microbiol Lett 2003; 219:275-83. [PMID: 12620632 DOI: 10.1016/s0378-1097(03)00028-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The first complete nucleotide sequences of two lytic Staphylococcus aureus double stranded DNA phages, 44AHJD (16784 bp) and P68 (18227 bp), are reported. Both are small isometric phages, with short, non-contractile tails and a pre-neck appendage. Based on their morphology, their genome size, the similarity of the encoded gene products, the type of infection and on the possession of a type B DNA polymerase, 44AHJD and P68 are allocated to the order Caudovirales, family Podoviridae, genus 'phi29-like phages'. The genome of 44AHJD differs from that of P68 by a deletion spanning nucleotides 10091 to 11531 of the P68 genome. The electrophoretic analysis of the terminal DNA fragments of P68 DNA and P68 DNA protein complex suggested the presence of a terminal protein at either DNA end. In contrast to the lysis cassette of the phi29-like phages, which is located at the end of the late operon, the lysis cassette of 44AHJD and P68 is located within the structural genes.
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Affiliation(s)
- Dietmar Vybiral
- Institute of Microbiology and Genetics, Vienna Biocenter, Dr. Bohr-Gasse 9, A-1030, Vienna, Austria
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14
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Oldenburg DJ, Bendich AJ. Mitochondrial DNA from the liverwort Marchantia polymorpha: circularly permuted linear molecules, head-to-tail concatemers, and a 5' protein. J Mol Biol 2001; 310:549-62. [PMID: 11439023 DOI: 10.1006/jmbi.2001.4783] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mapping predicts that the mitochondrial genome of the liverwort Marchantia polymorpha exists as a circular molecule, although nearly all the mitochondrial DNA (mtDNA) is found as genome-sized and multigenomic molecules in linear and branched form. We used restriction enzymes with one recognition site per genome, end-specific exonucleases and pulsed-field gel electrophoresis (PFGE) to analyze the arrangement of genomic units and the terminal structure of the molecules. We find a head-to-tail arrangement in the concatemers and circular permutation in both the monomeric and multigenomic molecules. The termini contain covalently bound protein at the 5' end and an open (unblocked) 3' end. We find that the standard in-gel procedure used to prepare large DNA molecules for PFGE may introduce extraction artifacts leading to erroneous conclusions about the termini. These artifacts can be reduced by omitting high salt (high EDTA) and protease during mitochondrial lysis. Our results suggest that the mtDNA may use a T4 phage-like mechanism of replication and that the linear molecules may be due to strand breaks mediated by type II topoisomerase.
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MESH Headings
- Artifacts
- DNA Replication
- DNA Restriction Enzymes/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA-Binding Proteins/metabolism
- Edetic Acid/pharmacology
- Electrophoresis, Gel, Pulsed-Field
- Endopeptidase K/metabolism
- Exodeoxyribonucleases/metabolism
- Genome
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Plant Cells
- Plant Proteins/metabolism
- Plants/genetics
- Salts/pharmacology
- Viral Proteins
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Affiliation(s)
- D J Oldenburg
- Department of Botany, University of Washington, Seattle, WA 98195-5325, USA
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15
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Peterson C, Simon M, Hodges J, Mertens P, Higgins L, Egelman E, Anderson D. Composition and mass of the bacteriophage phi29 prohead and virion. J Struct Biol 2001; 135:18-25. [PMID: 11562162 DOI: 10.1006/jsbi.2001.4375] [Citation(s) in RCA: 18] [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
The protein composition of the Bacillus subtilis bacteriophage phi29 prohead and virion was determined by combustion of gel bands of (3)H-labeled proteins. Copy numbers of individual proteins were calculated relative to the 12 copies of the head-tail connector protein. The mean numbers of copies of the major capsid protein in the prohead and virion were 241 and 218, respectively, approaching the 235 copies determined previously by cryoelectron microscopy. The mean numbers of copies of the dimeric head fiber on the prohead and virion were 24 and 31, respectively, demonstrating partial occupancy of the 55 fiber binding sites. Measured copies of neck and tail proteins in the virion included 11 of the lower collar, 58 of the appendage, and 9 of the tail; if the true copies of these proteins are 12, 60, and 9, respectively, the entire neck and tail of phi29 has quasi-sixfold symmetry. The mass of the fiberless prohead with pRNA was about 14.2 MDa, and the mass of the prohead determined by scanning transmission electron microscopy was consistent with the biochemical data. The mass of the fiberless virion containing the 12.8-MDa DNA genome was about 30.4 MDa. A full complement of dimeric fibers on the prohead or virion would increase the mass of the particle by about 3.2 MDa. The data complement studies relating the structure of phi29 components to dynamic functions in morphogenesis and infection.
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Affiliation(s)
- C Peterson
- Department of Oral Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
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16
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Meijer WJ, Lewis PJ, Errington J, Salas M. Dynamic relocalization of phage phi 29 DNA during replication and the role of the viral protein p16.7. EMBO J 2000; 19:4182-90. [PMID: 10921898 PMCID: PMC306615 DOI: 10.1093/emboj/19.15.4182] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have examined the localization of DNA replication of the Bacillus subtilis phage phi 29 by immunofluorescence. To determine where phage replication was localized within infected cells, we examined the distribution of phage replication proteins and the sites of incorporation of nucleotide analogues into phage DNA. On initiation of replication, the phage DNA localized to a single focus within the cell, nearly always towards one end of the host cell nucleoid. At later stages of the infection cycle, phage replication was found to have redistributed to multiple sites around the periphery of the nucleoid, just under the cell membrane. Towards the end of the cycle, phage DNA was once again redistributed to become located within the bulk of the nucleoid. Efficient redistribution of replicating phage DNA from the initial replication site to various sites surrounding the nucleoid was found to be dependent on the phage protein p16.7.
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Affiliation(s)
- W J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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17
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Polo S, Guerini O, Sosio M, Dehb G. Identification of two linear plasmids in the actinomycete Planobispora rosea. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2819-2825. [PMID: 9802023 DOI: 10.1099/00221287-144-10-2819] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two linear plasmids (pPR1, 27.5 kb, and pPR2, 16 kb) were identified in Planobispora rosea, an actinomycete that produces the antibiotic GE2270, an inhibitor of the elongation factor Tu. Strains lacking both plasmids still produce and are resistant to GE2270. The two plasmids share an internal region of high similarity, but no cross-hybridization was detected between their telomeric regions or between plasmid and chromosomal DNA. The 5' ends of the plasmids appear to be linked to terminal proteins. The telomeric regions of pPR2 were cloned after 3'-end homopolymer tailing and PCR amplification. The approximately 650 nt telomeric DNA sequences of pPR2 are repeated in inverted orientation and are rich in direct and inverted repeats; the 350 bp terminal region is less G + C-rich than the rest of the plasmid. The structural organization of these plasmids appears to be similar to Streptomyces linear replicons.
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Affiliation(s)
- Simona Polo
- Dipartimento di Geneticae di Biologia dei Microrganismi, Universita degli Studi di MilanoVia Celoria 26, 20133 MilanoItaly
| | - Oscar Guerini
- Dipartimento di Geneticae di Biologia dei Microrganismi, Universita degli Studi di MilanoVia Celoria 26, 20133 MilanoItaly
| | | | - Gianni Dehb
- Dipartimento di Geneticae di Biologia dei Microrganismi, Universita degli Studi di MilanoVia Celoria 26, 20133 MilanoItaly
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18
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Zhu W, Ito J. Family A and family B DNA polymerases are structurally related: evolutionary implications. Nucleic Acids Res 1994; 22:5177-83. [PMID: 7816603 PMCID: PMC332057 DOI: 10.1093/nar/22.24.5177] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In order to establish the evolutionary relationship between the family A and B DNA polymerases, we have closely compared the 3'-->5' exonuclease domains between the Klenow fragment of E.coli DNA polymerase I (a family A DNA polymerase) and the bacteriophage PRD1 DNA polymerase, the smallest member of the DNA polymerase family B. Although the PRD1 DNA polymerase has a smaller 3'-->5' exonuclease domain, its active sites appear to be very similar to those of the Klenow fragment. Site-directed mutagenesis studies revealed that the residues important for the 3'-->5' exonuclease activity, particularly metal binding ligands for the Klenow fragment, are all conserved in the PRD1 DNA polymerase as well. The metal binding ligands are also essential for the strand-displacement activity of the PRD1 DNA polymerase. Based on these results and the studies by others in various systems, we conclude that family A and B DNA polymerases, at least in the 3'-->5' exonuclease domain, are structurally as well as evolutionarily related.
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Affiliation(s)
- W Zhu
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, Tucson 85724
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19
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Zhu W, Leavitt MC, Jung G, Ito J. Mutagenesis of a highly conserved lysine 340 of the PRD1 DNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:260-6. [PMID: 7918620 DOI: 10.1016/0167-4781(94)90047-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
All known family B DNA polymerases contain a conserved region of amino acids, KX6-7YG, which appears to be correspond to the 'finger' alpha helix O of the Klenow fragment of E. coli DNA polymerase I, a family A DNA polymerase. Toward the goal of establishing the evolutionary relationship between the family A and B DNA polymerases, we have employed site-directed mutagenesis to access the functional role of the invariant amino acid lysine-340 of the PRD1 DNA polymerase. We have replaced the lysine-340 with three amino acids: histidine, asparagine and glutamic acid, respectively. Mutant DNA polymerases were overexpressed and purified to near homogeneity. Our results showed that the modification of the lysine-340 of the PRD1 DNA polymerase abolishes the polymerase activity without affecting the 3' to 5' exonuclease activity. These results support the proposal that the KX6-7YG motif of the family B DNA polymerases may be analogous to the KX7YG motif of the family A DNA polymerases, suggesting that two family DNA polymerases share a common ancestor.
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Affiliation(s)
- W Zhu
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, Tucson 85724
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20
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Zhu W, Ito J. Purification and characterization of PRD1 DNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1219:267-76. [PMID: 7918621 DOI: 10.1016/0167-4781(94)90048-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A small lipid-containing bacteriophage PRD1 encodes a DNA polymerase that utilizes a protein primer for the initiation of DNA replication. The purification of the PRD1 DNA polymerase has been hampered by the insolubility of the overexpressed enzyme in Escherichia coli cells. We have developed a simple and rapid procedure for purification of the overexpressed PRD1 DNA polymerase. This method is based on guanidine hydrochloride denaturation and renaturation of the insoluble PRD1 DNA polymerase overexpressed in E. coli containing the recombinant plasmid pEJG. The purified DNA polymerase was extensively characterized and found to be indistinguishable from the normal soluble PRD1 DNA polymerase as judged by enzymatic properties. These properties include: protein-primed initiation of PRD1 DNA replication, strand-displacement DNA synthesis, DNA polymerase processivity, 3' to 5' exonuclease activity and filling-in repair type DNA synthesis. Furthermore, the kinetic parameters determined for dNTPs and primer-terminus were of the same order of magnitude. The availability of a simple purification procedure for the PRD1 DNA polymerase should permit detailed structure-function analysis of this enzyme.
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Affiliation(s)
- W Zhu
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, Tucson 85724
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21
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Steiner M, Lubitz W, Bläsi U. The missing link in phage lysis of gram-positive bacteria: gene 14 of Bacillus subtilis phage phi 29 encodes the functional homolog of lambda S protein. J Bacteriol 1993; 175:1038-42. [PMID: 8432697 PMCID: PMC193017 DOI: 10.1128/jb.175.4.1038-1042.1993] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In most bacteriophages of gram-negative bacteria, the phage endolysin is released to its murein substrate through a lesion in the inner membrane. The lesion is brought about by a second phage-encoded lysis function. For the first time, we present evidence that the same strategy is elaborated by a phage of a gram-positive bacterium. Thus, there appears to be an evolutionarily conserved lysis pathway for most phages whether their host bacterium is gram negative or gram positive. Phage phi 29 gene 14, the product of which is required for efficient lysis of Bacillus subtilis, was cloned in Escherichia coli. Production of protein 14 in E. coli resulted in cell death, whereas production of protein 14 concomitantly with the phi 29 lysozyme or unrelated murein-degrading enzymes led to lysis, suggesting that membrane-bound protein 14 induces a nonspecific lesion in the cytoplasmic membrane.
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Affiliation(s)
- M Steiner
- Institute of Microbiology and Genetics, University of Vienna, Austria
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22
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Kinashi H, Shimaji-Murayama M, Hanafusa T. Integration of SCP1, a giant linear plasmid, into the Streptomyces coelicolor chromosome. Gene 1992; 115:35-41. [PMID: 1319377 DOI: 10.1016/0378-1119(92)90537-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
SCP1, coding for the methylenomycin biosynthetic genes in Streptomyces coelicolor, is a giant linear plasmid of 350 kb. Extensive physical characterization revealed that SCP1 has unusually long terminal inverted repeats (TIR) of about 80 kb on both ends and an insertion sequence, IS466, at the end of the right TIR (TIR-R), and the 5'-ends are attached to a terminal protein. In the NF strain S. coelicolor 2612, SCP1 is integrated into the chromosome at the 9-o'clock position. Analysis of the two junctions between the SCP1 DNA and the chromosomal DNA revealed that the left junction had an almost intact left terminus of SCP1, while the right junction was composed of IS466, completely deleting TIR-R. Based on these results, we presented a possible formation mechanism of the NF strain, which is characterized by integration of SCP1 into the chromosome via an interaction of the target site and the combined ends of the racket-frame structure of SCP1 followed by deletion of TIR-R. We also hypothesized that this type of integration of a giant linear plasmid might be involved in the origin and distribution of the chromosomal antibiotic biosynthetic gene clusters in microorganisms.
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Affiliation(s)
- H Kinashi
- Department of Fermentation Technology, Faculty of Engineering, Hiroshima University, Higashihiroshima, Japan
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23
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Kinashi H, Shimaji-Murayama M, Hanafusa T. Nucleotide sequence analysis of the unusually long terminal inverted repeats of a giant linear plasmid, SCP1. Plasmid 1991; 26:123-30. [PMID: 1749818 DOI: 10.1016/0147-619x(91)90052-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
SCP1 is a giant linear plasmid of 350 kb coding for the methylenomycin biosynthetic genes in Streptomyces coelicolor. The unusually long terminal inverted repeats present on both ends of SCP1 were analyzed on the nucleotide sequence level. Analysis of six clones containing the terminal 0.35-kb XbaI fragment revealed a slight heterogeneity in the nucleotide sequences of the SCP1 ends. Moreover, it was indicated that this fragment contained seven palindromic inverted repeats and a GT-rich region in the 5'-end strand. The size of the terminal inverted repeats was determined to be 81 kb by the cloning and sequencing of their end-points. An insertion sequence, IS466 was shown to be present just at the end of the right terminal inverted repeat.
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Affiliation(s)
- H Kinashi
- Mitsubishi Kasei Institute of Life Sciences, Tokyo, Japan
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24
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Kinashi H, Shimaji-Murayama M. Physical characterization of SCP1, a giant linear plasmid from Streptomyces coelicolor. J Bacteriol 1991; 173:1523-9. [PMID: 1847368 PMCID: PMC207291 DOI: 10.1128/jb.173.4.1523-1529.1991] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SCP1, coding for the methylenomycin biosynthesis genes in Streptomyces coelicolor, was shown to be a giant linear plasmid of 350 kb with a copy number of about four by analysis with pulsed-field gel electrophoresis. A detailed physical map of SCP1 was constructed by extensive digestion with six restriction endonucleases, by DNA hybridization experiments, and finally by cloning experiments. SCP1 has unusually long terminal inverted repeats of 80 kb on both ends and an insertion sequence at the end of the right terminal inverted repeat. Analysis by pulsed-field gel electrophoresis in agarose containing sodium dodecyl sulfate revealed that a protein is bound to the terminal 4.1-kb SpeI fragments derived from both ends of SCP1. Treatment with lambda exonuclease or exonuclease III and SpeI digestion also indicated that the 5' ends of SCP1 are attached to a protein.
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Affiliation(s)
- H Kinashi
- Mitsubishi Kasei Institute of Life Sciences, Tokyo, Japan
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25
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Abstract
A cell-free system has been developed from cells of an Escherichia coli strain, carrying cloned genes 1 and 8 of bacteriophage PRD1, that catalyzes protein-primed DNA synthesis. DNA synthesis in vitro is entirely dependent upon the addition of PRD1 DNA-protein complex as template, Mg2+, and four deoxyribonucleoside triphosphates. No in vitro DNA synthesis was observed when deproteinized PRD1 DNA was used as template. The origin and direction of PRD1 DNA replication in vitro was determined by restriction enzyme analysis of 32P-labeled PRD1 DNA synthesized in this system. Replication starts at both ends of the linear PRD1 DNA template. Alkaline sucrose gradient centrifugation and agarose gel electrophoresis showed that full-length PRD1 DNA is synthesized in vitro. DNA synthesis in this system is inhibited by the drug aphidicolin. We also observed that dimethyl sulfoxide (DMSO) stimulates in vitro DNA synthesis, although it inhibits bacterial DNA polymerase.
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Affiliation(s)
- S K Yoo
- Department of Microbiology and Immunology, University of Arizona Health Sciences Center, Tucson 85724
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26
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Zaballos A, Mellado RP, Salas M. Initiation of phage phi 29 DNA replication by mutants with deletions at the amino end of the terminal protein. Gene X 1988; 63:113-21. [PMID: 3133284 DOI: 10.1016/0378-1119(88)90550-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Series of deletions at the amino end of protein p3, the phage phi 29 DNA terminal protein (TP), have been constructed and characterized. Measurements of the activity of the deletion mutants in the formation of the protein p3-dAMP initiation complex in vitro indicate the dispensability of the first 13 amino acids (aa) of the protein. The activity of protein p3 decreased considerably when 17 or more aa were deleted. The results on the in vitro phi 29 DNA replication primed by the p3 deletion mutants correlated very well with those obtained in the formation of the TP-dAMP initiation complex.
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Affiliation(s)
- A Zaballos
- Centro de Biología Molecular (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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27
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Salas M. Initiation of DNA replication by primer proteins: bacteriophage phi 29 and its relatives. Curr Top Microbiol Immunol 1988; 136:71-88. [PMID: 3131070 DOI: 10.1007/978-3-642-73115-0_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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28
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Abstract
The nucleotide sequence of Bacillus phage Nf gene E has been determined. Gene E codes for phage terminal protein which is the primer necessary for the initiation of DNA replication. The deduced amino acid sequence of Nf terminal protein is approximately 66% homologous with the terminal proteins of Bacillus phages PZA and luminal diameter 29, and shows similar hydropathy and secondary structure predictions. A serine which has been identified as the residue which covalently links the protein to the 5' end of the genome in luminal diameter 29, is conserved in all three phages. The hydropathic and secondary structural environment of this serine is similar in these phage terminal proteins and also similar to the linking serine of adenovirus terminal protein.
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29
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Saedi MS, Yoo SK, Watabe K, Garvey KJ, Ito J. Characterization of a deletion mutant of bacteriophage phi 29. Virology 1987; 158:313-9. [PMID: 3590622 DOI: 10.1016/0042-6822(87)90203-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A spontaneous deletion mutant of bacteriophage phi 29 (phi 29 delta 1) has been characterized. This mutant has a 1112-bp deletion, which covers almost the entire sequence of genes 14 and 15, including an early promoter (B2). While lysis is very delayed, the phage DNA synthesis and internal phage development appear to be normal in the cells infected with this deletion mutant. These results indicate that the early functions are intact in phi 29 delta 1. Our results also suggest that genes 14 and 15 are dispensable for bacteriophage phi 29 growth and that the B2 promoter may also be dispensable for early functions in phi 29.
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30
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Guo PX, Erickson S, Anderson D. A small viral RNA is required for in vitro packaging of bacteriophage phi 29 DNA. Science 1987; 236:690-4. [PMID: 3107124 DOI: 10.1126/science.3107124] [Citation(s) in RCA: 268] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A small RNA of Bacillus subtilis bacteriophage phi 29 is shown to have a novel and essential role in viral DNA packaging in vitro. This requirement for RNA in the encapsidation of viral DNA provides a new dimension of complexity to the attendant protein-DNA interactions. The RNA is a constituent of the viral precursor shell of the DNA-packaging machine but is not a component of the mature virion. Studies of the sequential interactions involving this RNA molecule are likely to provide new insight into the structural and possible catalytic roles of small RNA molecules. The phi 29 assembly in extracts and phi 29 DNA packaging in the defined in vitro system were strongly inhibited by treatment with the ribonucleases A or T1. However, phage assembly occurred normally in the presence of ribonuclease A that had been treated with a ribonuclease inhibitor. An RNA of approximately 120 nucleotides co-purified with the phi 29 precursor protein shell (prohead), and this particle was the target of ribonuclease action. Removal of RNA from the prohead by ribonuclease rendered it inactive for DNA packaging. By RNA-DNA hybridization analysis, the RNA was shown to originate from a viral DNA segment very near the left end of the genome, the end packaged first during in vitro assembly.
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31
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32
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Saedi MS, Garvey KJ, Ito J. Cloning and purification of a unique lysozyme produced by Bacillus phage phi 29. Proc Natl Acad Sci U S A 1987; 84:955-8. [PMID: 3469652 PMCID: PMC304338 DOI: 10.1073/pnas.84.4.955] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A DNA fragment of the bacteriophage phi 29 chromosome, encoding the entire sequence of phi 29 gene 15, has been cloned into the Escherichia coli expression vector pPLc245 under the control of the phage lambda major leftward promoter, PL. Upon heat induction, a protein with an apparent molecular mass of 26 kDa was overproduced. The molecular mass of this protein corresponds to the 28 kDa predicted for the product of gene 15 from its nucleotide sequence. The overproduced protein has been purified to near homogeneity and confirmed to be the product of gene 15 by amino acid sequence analysis of its N terminus. The purified product of gene 15 has a lysozyme activity similar to other phage-type lysozymes: products of phage T4 gene e and of phage P22 gene 19. However, to our knowledge phi 29 lysozyme is structurally unique among the phage-type lysozymes.
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33
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Analysis of a linear plasmid isolated from the pathogenic fungus Ceratocystis fimbriata Ell. & Halst. Curr Genet 1987. [DOI: 10.1007/bf00355409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Vartapetian AB, Bogdanov AA. Proteins covalently linked to viral genomes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1987; 34:209-51. [PMID: 3326040 DOI: 10.1016/s0079-6603(08)60497-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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35
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Whiteley HR, Ramey WD, Spiegelman GB, Holder RD. Modulation of in vivo and in vitro transcription of bacteriophage phi 29 early genes. Virology 1986; 155:392-401. [PMID: 3097957 DOI: 10.1016/0042-6822(86)90202-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The majority of early transcripts of the phi 29 bacteriophage are produced throughout the lytic cycle but the levels of a class of transcripts from the right end of the phi 29 genome are significantly reduced late in the infection. We have isolated a phage early protein which selectively interferes with the initiation in vitro of transcription from promoters at the right end of the phi 29 genome. The amino acid sequence of the purified inhibitory protein correlates to the sequence predicted from the phi 29 gene 6 reading frame. In addition the inhibitory protein was not detectable in cells infected with phage mutated in gene 6 and the decrease in transcription did not occur in vivo when nonpermissive cells were infected with phi 29(sus6). The results indicate that the gene 6 protein modulates transcription from the right side of the phi 29 genome.
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36
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Rist JK, Pearle M, Sugino A, Rothman-Denes LB. Development of an in vitro bacteriophage N4 DNA replication system. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67413-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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37
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38
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Zaballos A, Salas M, Mellado RP. Initiation of phage phi 29 DNA replication by mutants with deletions at the carboxyl end of the terminal protein. Gene 1986; 43:103-10. [PMID: 3019830 DOI: 10.1016/0378-1119(86)90013-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Series of deletions at the C end of p3, the phage phi 29 DNA terminal protein (TP), have been constructed and characterized. Measurements of the activity of those deletion mutants in the formation of the p3-dAMP initiation complex in vitro indicate the need of an intact C-end for the normal TP primer function in DNA replication. It appears that the region at the C-end between aa 240 and 262 of p3, or part of it, might be essential for the normal TP function.
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39
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Blanco L, Salas M. Replication of phage phi 29 DNA with purified terminal protein and DNA polymerase: synthesis of full-length phi 29 DNA. Proc Natl Acad Sci U S A 1985; 82:6404-8. [PMID: 3863101 PMCID: PMC390724 DOI: 10.1073/pnas.82.19.6404] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A system that replicates bacteriophage phi 29 DNA with protein p3 covalently attached to the two 5' ends, using as the only proteins the phi 29 DNA polymerase and the terminal protein, is described. Restriction analysis of the 32P-labeled DNA synthesized in vitro showed that all phi 29 DNA fragments were labeled. Analysis by alkaline sucrose gradient centrifugation of the DNA labeled during a 10-min pulse showed that, after a 20-min chase, about half of the DNA molecules had reached apparently full-length phi 29 DNA (approximately equal to 18,000 nucleotides). Ammonium ions strongly stimulated phi 29 DNA-protein p3 replication, the effect being due to stimulation of the initiation reaction. ATP was not required for phi 29 DNA-protein p3 replication, either in the initiation or elongation steps. The results show that the phi 29 DNA polymerase functions, not only in the formation of the p3-dAMP covalent initiation complex but also in the elongation of the latter, as the only DNA polymerase to produce full-length phi 29 DNA.
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40
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Kikuchi Y, Hirai K, Gunge N, Hishinuma F. Hairpin plasmid--a novel linear DNA of perfect hairpin structure. EMBO J 1985. [PMID: 2992950 PMCID: PMC554431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The terminal structures of deletion derivatives of linear DNA killer plasmid from yeast were analyzed. The yeast Kluyveromyces lactis harbors two unique double-stranded linear DNA killer plasmids, pGKL1 of 8.9 kb and pGKL2 of 13.4 kb. The killer toxin and the resistance to the killer are coded by pGKL1, while pGKL2 is required for the maintenance of pGKL1 in the cell. When the pGKL plasmids from K. lactis were transferred into Saccharomyces cerevisiae by transformation, non-killer transformants harboring pGKL2 and new plasmids, F1 of 7.8 kb and F2 of 3.9 kb, were obtained. F2 was shown to be a linear DNA arising from a 5-kb deletion of the right part of pGKL1. F1 was an inverted dimer of F2. Here we show that F2 has two different terminal structures: one end has a protein attached at the 5' terminus whereas the two strands of duplex are linked together at the other end, thus forming a hairpin structure. This is a novel type of autonomously replicating DNA molecule.
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41
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Pastrana R, Lázaro JM, Blanco L, García JA, Méndez E, Salas M. Overproduction and purification of protein P6 of Bacillus subtilis phage phi 29: role in the initiation of DNA replication. Nucleic Acids Res 1985; 13:3083-100. [PMID: 3158884 PMCID: PMC341222 DOI: 10.1093/nar/13.9.3083] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A phi 29 DNA fragment containing gene 6, required for DNA replication, has been cloned in plasmid pPLc28 under the control of the PL promoter of phage lambda. A polypeptide with an electrophoretic mobility close to that of p6 was labelled with 35S-methionine after heat induction. This protein, representing about 4% of the total E. coli protein after 1 h of induction, was obtained in a highly purified form. The protein was characterized as p6 by amino acid analysis and NH2-and COOH-terminal sequence determination. Protein p6 has an apparent molecular weight of 23,600, suggesting that the native form of the protein is a dimer. The purified protein p6 stimulated the protein-primed initiation of phi 29 DNA replication when added to purified proteins p2 (phi 29-coded DNA polymerase) and p3 (terminal protein).
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42
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Dobinson KF, Spiegelman GB. Nucleotide sequence and transcription of a bacteriophage 29 early promoter. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88921-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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43
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Paillard M, Sederoff RR, Levings CS. Nucleotide sequence of the S-1 mitochondrial DNA from the S cytoplasm of maize. EMBO J 1985; 4:1125-8. [PMID: 16453611 PMCID: PMC554313 DOI: 10.1002/j.1460-2075.1985.tb03749.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mitochondria from the S male-sterile cytoplasm of maize contain unique DNA-protein complexes, designated S-1 and S-2. These complexes consist of double-stranded linear DNAs with proteins covalently attached to the 5' termini. To learn more about these unusual DNAs we have determined the complete nucleotide sequence of the S-1 DNA molecule (6397 bp). The sequence of S-2 has been previously determined. S-1 and S-2 are structurally similar and contain 1.7kb of sequence homology. S-1 is terminated by exact 208-bp inverted repeats that are identical with the terminal inverted repeats of S-2. S-1 and S-2 also contain a 1462-bp region of nearly perfect homology, which includes one of the terminal inverted repeats. The homology between the two molecules may be maintained, in part, by homologous recombination. S-1 has three long unidentified open reading frames, URF2 (1017 bp), URF3 (2787 bp) and URF4 (768 bp). URF2 occurs in the 1462-bp region of homology and is identical in length and location in both S-1 and S-2. Based on their structural organization and their viral-like characteristics, we propose that S-1 and S-2 code for functions involved with their maintenance and replication.
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Affiliation(s)
- M Paillard
- Department of Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
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44
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Blanco L, Salas M. Characterization of a 3'----5' exonuclease activity in the phage phi 29-encoded DNA polymerase. Nucleic Acids Res 1985; 13:1239-49. [PMID: 2987819 PMCID: PMC341069 DOI: 10.1093/nar/13.4.1239] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purified protein p2 of phage phi 29, characterized as a specific DNA polymerase involved in the initiation and elongation of phi 29 DNA replication, contains a 3'----5' exonuclease active on single-stranded DNA, but not on double-stranded DNA. No 5'----3' exonuclease activity was found. The 3'----5' exonuclease activity was shown to be associated with the DNA polymerase since 1) the two activities were heat-inactivated with identical kinetics and 2) both activities, present in purified protein p2, cosedimented in a glycerol gradient.
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45
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Linear plasmids with terminal inverted repeats obtained from Streptomyces rochei and Kluyveromyces lactis. BASIC LIFE SCIENCES 1985; 30:433-51. [PMID: 2990421 DOI: 10.1007/978-1-4613-2447-8_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Linear plasmids with inverted terminal repeats of 614 bp were obtained from Streptomyces rochei which produced lankacidin. The 5' ends were blocked by the association of a terminal protein. A DNA model of racket frame-like structure is presented implying the juxtaposition of 2 double-stranded DNAs of the same sequence through the binding of cohesive proteins which recognize and bind to the DNA. Two linear plasmids with the inverted terminal repeats of 202 and 184 bp were obtained from a yeast, Kluyveromyces lactis. A killer toxin was produced from the shorter plasmid. The protein toxin inhibited the adenylatecyclase activity of the yeast membrane.
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46
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Yoshikawa H, Garvey KJ, Ito J. Nucleotide sequence analysis of DNA replication origins of the small Bacillus bacteriophages: evolutionary relationships. Gene 1985; 37:125-30. [PMID: 3932129 DOI: 10.1016/0378-1119(85)90264-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ends of the small Bacillus phage genomes serve as origins and termini of their DNA replication. We have determined nucleotide sequences at the termini of four different phage DNAs and compared them with those of phi 29 DNA which has been described previously. A high degree of homology was found at the extreme ends of DNAs from phi 29, phi 15 (group A), M2Y and Nf (group B). 17 bp at the far left of the DNAs are identical. A highly conserved dodecanucleotide sequence, CCATTTCCCCAT, was also found in the righthand terminus of all these phage DNAs, at positions 27-38 from the end. Nucleotide sequences of phage GA-1 are not very similar to those of the other phages. Examination of the 5'-terminal and 3'-terminal sequences of all the phages suggests that stable 'panhandle' structures are unlikely to be formed via base pairing of both ends. However, thermodynamically more stable panhandle structures might be formed by displaced single-stranded DNA, although this requires rather large loops.
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47
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Escarmis C, García P, Méndez E, López R, Salas M, García E. Inverted terminal repeats and terminal proteins of the genomes of pneumococcal phages. Gene X 1985; 36:341-8. [PMID: 3000885 DOI: 10.1016/0378-1119(85)90189-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The nucleotide (nt) sequence at the ends of the genomes of the Streptococcus pneumoniae phages Cp-5 and Cp-7 has been determined and compared with the corresponding sequence of phage Cp-1. The genomes of phages Cp-5 and Cp-7 have inverted terminal repeats (ITRs) 343 and 347 bp long, respectively. In Cp-1 DNA the ITR is 236 bp long and the following 116 bp are 93% homologous. Some regions within the ITRs are conserved in the three genomes although the complete sequence of the ITRs is no more conserved than the rest of their genomes. The chromatographic behavior of their tryptic peptides suggests that the terminal proteins (TPs) of at least two of the phages are similar and that the TPs of the three pneumococcal phages differ markedly from that of the Bacillus subtilis phage psi 29.
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48
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49
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Blanco L, Salas M. Characterization and purification of a phage phi 29-encoded DNA polymerase required for the initiation of replication. Proc Natl Acad Sci U S A 1984; 81:5325-9. [PMID: 6433348 PMCID: PMC391696 DOI: 10.1073/pnas.81.17.5325] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The phage phi 29 protein p2, required for the formation of the protein p3-dAMP initiation complex, has been purified from Escherichia coli cells harboring a gene 2-containing recombinant plasmid. The purified protein p2, of molecular weight 68,000, had a specific DNA polymerase activity that elongated the p3-dAMP initiation complex when phi 29 DNA-protein p3 was used as template. In addition, the purified protein p2 was active in catalyzing the initiation reaction when complemented with phi 29 mutant sus2-infected Bacillus subtilis or plasmid-containing E. coli extracts providing protein p3, in the presence of phi 29 DNA-protein p3 as template. However, when purified protein p3 was used in the complementation assay, a very low amount of initiation complex was formed; addition of extracts from uninfected B. subtilis or E. coli strongly stimulated the initiation reaction, indicating that, in addition to proteins p2 and p3 and the phi 29 DNA-protein p3 template, some host factor(s) is required for the formation of the p3-dAMP initiation complex. The results show that phage phi 29 encodes a DNA polymerase that is required at the initiation step of protein-primed DNA synthesis.
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50
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Prieto I, Lázaro JM, García JA, Hermoso JM, Salas M. Purification in a functional form of the terminal protein of Bacillus subtilis phage phi 29. Proc Natl Acad Sci U S A 1984; 81:1639-43. [PMID: 6424120 PMCID: PMC344973 DOI: 10.1073/pnas.81.6.1639] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Phage phi 29 terminal protein, p3, essentially pure, was isolated in a denatured form from viral particles, and anti-p3 antiserum was obtained. A radioimmunoassay to detect and quantitate protein p3 was developed. By using this assay, native protein p3 was highly purified from Escherichia coli cells harboring a gene 3-containing recombinant plasmid. After three purification steps, the protein was more than 96% pure; its amino acid composition was very similar to that deduced from the nucleotide sequence of gene 3. The purified protein was active in the formation of the covalent p3-dAMP initiation complex when supplemented with extracts of B. subtilis infected with a sus mutant of phi 29 in gene 3. No DNA polymerase or ATPase activities were present in the final preparation of protein p3.
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