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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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2
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Krawiec S, Jiménez F, García JA, Villanueva N, Sogo J, Salas M. The orderly, in vitro emergence of DNA from bacteriophage phi29 particles. Virology 2008; 111:440-54. [PMID: 18635055 DOI: 10.1016/0042-6822(81)90347-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/1980] [Indexed: 10/26/2022]
Abstract
phi29 DNA-containing 12-13- particles (produced by infecting nonsuppressor hosts of Bacillus subtilis with phage containing suppressible mutations in cistrons 12 and 13) can be complemented with lysates containing proteins p12* and p13 to yield infectious phage. Complementation of these particles with lysates containing p12* but not p13 or complementation with purified p12* in the absence of p13 produces a structure (called complex) which has a markedly different organization. Electron microscopy and sedimentation analysis after digestion with DNase I or proteinase K indicate that complex is composed of an intact phage head with a genome-sized linear DNA molecule attached at the collar-tail region. EcoRI digestion establishes that the DNA molecule has a unique orientation. Gel electrophoresis indicates that p12*, the neck appendage protein, is transferred to the particles when complex is formed. Complex can also be produced by incubation of 12-13- particles at 42 degrees , by incubation at pH 6.0, or by incubation in the presence of 20 mM EDTA. Complex is also formed from DNA-containing 12- particles but to a lesser extent.
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Affiliation(s)
- S Krawiec
- Centro de Biología Molecular (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Canto Blanco, Madrid-34, Spain
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Palmieri C, Trimboli F, Scala G, Quinto I, Bressler PB. Regulation of the HIV promoter/enhancer. CURRENT PROTOCOLS IN IMMUNOLOGY 2008; Chapter 12:Unit 12.7. [PMID: 18432898 DOI: 10.1002/0471142735.im1207s54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit describes adaptations of two molecular techniques that can be used to study the regulation of HIV expression. The first two protocols describe the chloramphenicol acetyltransferase (CAT) assay, in which the CAT reporter gene is attached to an HIV-1 promoter and CAT activity is measured as an indication of the promoter's activity. The basic protocol is rapid, simple, and suited to analyzing multiple samples. An alternate protocol describes an assay for CAT function that involves separating the reaction products by thin-layer chromatography (TLC). The second basic protocol describes an electrophoretic mobility shift assay for detecting proteins present in cell extracts that can bind to the HIV-1 LTR (long terminal repeat). Such studies are central to current HIV research because it is important to know what agents induce and inhibit (or "down-regulate") HIV transcription.
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Affiliation(s)
- Camillo Palmieri
- Department of Clinical and Experimental Medicine, University of Catanzaro, Magna Grecia, Cantazaro, Italy
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4
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Juodka BA. Covalent Interaction of Proteins and Nucleic Acids. Synthetic and Natural Nucleotide-Peptides. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328318408081283] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zotchev SB, Soldatova LI, Orekhov AV, Schrempf H. Characterization of a linear extrachromosomal DNA element (pBL1) isolated after interspecific mating between Streptomyces bambergiensis and S. lividans. Res Microbiol 1992; 143:839-45. [PMID: 1299837 DOI: 10.1016/0923-2508(92)90071-u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Streptomyces bambergiensis S712 harbours a giant linear plasmid PSB1 of 640 kb. After mating with the plasmidless S. lividans strain TK64, conjugants carrying a smaller extrachromosomal DNA element, pBL1, were identified. pBL1 is a 43-kb linear DNA molecule bound to a protein which protects it from attack by both 3'- and 5'-exonucleases. The absence of this protein drastically reduces the transforming efficiency of pBL1. pBL1 shares homology with linear plasmids and chromosomal DNA from S. bambergiensis strains.
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6
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Grimes S, Anderson D. In vitro packaging of bacteriophage phi 29 DNA restriction fragments and the role of the terminal protein gp3. J Mol Biol 1989; 209:91-100. [PMID: 2530357 DOI: 10.1016/0022-2836(89)90172-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Restriction fragments of bacteriophage phi 29 DNA-gp3 (DNA-gene product 3 complex) were packaged in a completely defined in vitro system that included purified proheads, the DNA packaging protein gp16 and ATP. Both left and right end DNA-gp3 fragments were packaged in this system, in contrast to the oriented and selective packaging of left end DNA-gp3 fragments in extracts; left ends could be packaged quantitatively in the defined system, while the packaging efficiency of right ends was generally about threefold lower. In addition, certain internal (non-end) DNA fragments were packaged at efficiencies of about 10% to 15%. Digestion of the gp3 with trypsin or proteinase K reduced the packaging of whole-length DNA by a factor of 2 or 4, respectively, and removal of the gp3 from whole-length DNA or end fragments with piperidine reduced packaging to the level of internal fragments. Though the terminal protein gp3 was non-essential for DNA translocation in the defined system, it stimulated packaging of left and right end fragments, and stabilized packaging of the left end. The packaging of end and internal DNA fragments of the related phage M2Y into phi 29 proheads was similar to that of phi 29 DNA fragments, and certain fragments of lambda DNA were packaged at the efficiency of the internal phi 29 DNA fragments. Selective packaging of DNA-gp3 left ends was restored by the addition of bacterial cell extracts or glycerol to the defined system, and these packaging conditions discriminated between phi 29 and M2Y DNAs that have distinct terminal proteins.
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Affiliation(s)
- S Grimes
- Department of Microbiology, University of Minnesota, Minneapolis 55455
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7
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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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8
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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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9
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Zaghloul TI, Doi RH. In vitro expression of a Tn9-derived chloramphenicol acetyltransferase gene fusion by using a Bacillus subtilis system. J Bacteriol 1987; 169:1212-6. [PMID: 3102458 PMCID: PMC211921 DOI: 10.1128/jb.169.3.1212-1216.1987] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A coupled in vitro protein-synthesizing system has been developed with components derived totally from Bacillus subtilis. The system synthesized specific gene products from various exogenous DNA templates, including B. subtilis phage phi 29, plasmid pUB110, and a heterologous B. subtilis-Escherichia coli gene fusion containing the transposon Tn9-derived chloramphenicol acetyltransferase (cat) gene. The gene fusion product was able to show CAT activity, bind specifically to a Sephacryl-chloramphenicol column, and react immunologically against anti-CAT antiserum. The fidelity of this in vitro system was demonstrated by the synthesis of gene products identical to that made in vivo. We suggest that this system may be used to study the regulation of gene expression in vitro.
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10
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Chow M, Bodnar JW, Polvino-Bodnar M, Ward DC. Identification and characterization of a protein covalently bound to DNA of minute virus of mice. J Virol 1986; 57:1094-104. [PMID: 2936897 PMCID: PMC252843 DOI: 10.1128/jvi.57.3.1094-1104.1986] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We identified a protein which is covalently linked to a fraction of the DNA synthesized in cells infected with minute virus of mice. This protein is specifically bound to the 5' terminus of the extended terminal conformers of the minute virus of mice replicative-form DNA species and of a variable fraction of single-stranded viral DNA. The chemical stability of the protein-DNA linkage is characteristic of a phosphodiester bond between a tyrosine residue in the protein and the 5' end of the DNA. The terminal protein (TP) bound on all DNA forms has a relative molecular weight of 60,000; it is also seen free in extracts from infected cells. Immunologic comparison of the TP with the other known viral proteins suggests that the TP is not related to the capsid proteins or NS-1.
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11
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Gibson W, Borst P, Fase-Fowler F. Further analysis of intraspecific variation in Trypanosoma brucei using restriction site polymorphisms in the maxi-circle of kinetoplast DNA. Mol Biochem Parasitol 1985; 15:21-36. [PMID: 2985985 DOI: 10.1016/0166-6851(85)90026-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have compared the maxi-circle kinetoplast DNA of 21 Trypanosoma brucei sp. stocks by analysis of restriction sites for nine restriction endonucleases. The analysis shows most of these stocks to have a maxi-circle sequence similar to that of 11 previously analysed stocks, with a difference of less than 3% between any two stocks. However, seven stocks stand out from the rest with at least two sites lost or gained for six of the nine restriction enzymes used. These seven distinctive stocks fall into two groups with some shared and some unique polymorphisms. One group had already been designated the kiboko group on the basis of isoenzyme patterns, but the relationship between nuclear markers and maxi-circle type is less clear-cut for the other group, designated sindo. Both groups seem to be in a wild animal-tsetse fly transmission cycle, with occasional infections in domestic stock, and may be reproductively isolated from the main T. brucei sp. population. The existence of the kiboko and sindo sub-groups shows that the maxi-circle is not shielded from evolutionary change. The lack of difference observed between the maxi-circles of the majority of T. brucei sp. stocks, including the gambiense and rhodesiense variants, must therefore reflect their close homology. Two geographical trends occur in T. brucei as a whole: (a) a trend in maxi-circle size, with increasing length of the variable region from West to East Africa, and (b) a greater frequency of certain restriction enzyme polymorphisms in East African stocks as compared to West African stocks.
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12
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Bakhiet N, Stahly DP. Studies on transfection and transformation of protoplasts of Bacillus larvae, Bacillus subtilis, and Bacillus popilliae. Appl Environ Microbiol 1985; 49:577-81. [PMID: 3922299 PMCID: PMC373552 DOI: 10.1128/aem.49.3.577-581.1985] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Protoplasts of Bacillus larvae NRRL b-3555 and Bacillus subtilis RM125 (restrictionless, modificationless mutant) were transfected with DNA from the B. larvae bacteriophage PBL1c in the presence of polyethylene glycol. B. subtilis 168 and Bacillus popilliae NRRL B-2309M protoplasts could not be transfected with PBL1c DNA. Protoplasts of B larvae NRRL B-3555 were transformed with plasmids pC194 and pHV33 in the presence of polyethylene glycol. The frequency of transformation was much higher when the plasmids were isolated from B. larvae NRRL B-3555 transformants than when they were isolated from B. subtilis 168. These results indicate that the restriction-modification systems found in B. larvae NRRL B-3555 and B. subtilis 168 may be different. Conditions for protoplast formation and cell wall regeneration were developed for B. popilliae NRRL B-2309S. However, no transformation occurred with plasmids pC194 and pHV33 (isolated from B. subtilis 168).
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13
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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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14
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Matsumoto K, Saito T, Hirokawa H. In vitro initiation of bacteriophage phi 29 and M2 DNA replication: genes required for formation of a complex between the terminal protein and 5'dAMP. MOLECULAR & GENERAL GENETICS : MGG 1983; 191:26-30. [PMID: 6310350 DOI: 10.1007/bf00330885] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell-free extracts prepared from phi 29 and M2-infected Bacillus subtilis cells catalyse the formation of complexes between terminal protein and [alpha-32P]-dAMP in the presence of [alpha-32P]-dATP, MgCl2, ATP, and phage DNA with terminal protein covalently linked at both the 5'ends. The complex formation does not take place when proteinase K-treated DNA is added or when uninfected extract is used. The phi 29 complex thus formed is smaller than the M2 complex, primarily due to the different molecular weights of the respective terminal proteins. Extracts prepared from cells infected with suppressor-sensitive mutants of genes 2 or 3 of phi 29 or genes G or E of M2 do not support complex formation. When the pair of extracts of phi 29 or M2-infected cells are mixed, however, formation of the complex takes place as a result of in vitro complementation. These results indicate that the complex formation observed in vitro reflects in vivo initiation of phage DNA replication. The product of gene 2 of phi 29 may be the enzyme that catalyses formation of the complex.
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15
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Bjornsti MA, Reilly BE, Anderson DL. Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: oriented and quantized in vitro packaging of DNA protein gp3. J Virol 1983; 45:383-96. [PMID: 6185695 PMCID: PMC256420 DOI: 10.1128/jvi.45.1.383-396.1983] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The assembly of phage phi 29 occurs by a single pathway, and the DNA protein (DNA-gp3) of "packaging intermediates" can be obtained after DNase I interruption of in vitro complementation. A broad spectrum of DNA molecules of variable length was isolated from DNase I-treated proheads. Restriction endonuclease EcoRI digestion and electrophoretic analysis of these DNA molecules suggested that DNA-gp3 packaging was oriented with respect to the physical map and was a complex process. Proteinase K-treated exogenous DNA was not packaged. When exogenous DNA-gp3 was predigested with the restriction endonucleases BstEII. EcoRI, HpaI, and HpaII, the left-end fragments, ranging in size from 8 to 0.9 megadaltons, were selectively and efficiently packaged. During in vivo and in vitro assembly, DNA-gp3 is packaged into proheads, the "core-scaffolding" protein gp7 exits from the particles, and the DNA-filled heads assume the angular morphology of phage phi 29. The packaging of a 4.1-megadalton DNA-gp3 left-end fragment (one third of the genome) resulted in the exit of gp7 and the transition to angularity.
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16
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Abstract
The nucleotide sequence of the left end of bacteriophage phi 29 DNA has been determined. Together with data reported earlier (Yoshikawa et al., 1981), this sequencing comprises the major early genetic region of this viral genome (5708 bp). Computer analysis of the DNA sequences revealed that there are up to fifteen open reading frames which could encode polypeptides containing more than thirty amino acids. The DNA sequence also revealed a number of potential regulatory signals, promoters and ribosome binding sites. The initiation and the termination of transcription and probable early gene products are discussed.
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17
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Bjornsti MA, Reilly BE, Anderson DL. Morphogenesis of bacteriophage phi 29 of Bacillus subtilis: DNA-gp3 intermediate in in vivo and in vitro assembly. J Virol 1982; 41:508-17. [PMID: 6804642 PMCID: PMC256779 DOI: 10.1128/jvi.41.2.508-517.1982] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The assembly of phage phi 29 occurs by a single pathway, and DNA-protein (DNA-gp3) has been shown to be an intermediate on the assembly pathway by a highly efficient in vitro complementation. At 30 degrees C, about one-half of the viral DNA synthesized was assembled into mature phage, and the absolute plating efficiency of phi 29 approached unity. DNA packaging at 45 degrees C was comparable to that at 30 degrees C, but the burst size was reduced by one-third. When cells infected with mutant ts3(132) at 30 degrees C to permit DNA synthesis were shifted to 45 degrees C before phage assembly, DNA synthesis ceased and no phage were produced. However, a variable amount of DNA packaging occurred. Superinfection by wild-type phage reinitiated ts3(132) DNA synthesis at 45 degrees C, and if native gp3 was covalently linked to this DNA during superinfection replication, it was effectively packaged and assembled. Treatment of the DNA-gp3 complex with trypsin prevented in vitro maturation of phi 29, although substantial DNA packaging occurred. A functional gp3 linked to the 5' termini of phi 29 DNA is a requirement for effective phage assembly in vivo and in vitro.
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18
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Hirochika H, Sakaguchi K. Analysis of linear plasmids isolated from Streptomyces: association of protein with the ends of the plasmid DNA. Plasmid 1982; 7:59-65. [PMID: 6283574 DOI: 10.1016/0147-619x(82)90027-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Borst P, Fase-Fowler F, Gibson WC. Quantitation of genetic differences between Trypanosoma brucei gambiense, rhodesiense and brucei by restriction enzyme analysis of kinetoplast DNA. Mol Biochem Parasitol 1981; 3:117-31. [PMID: 6166860 DOI: 10.1016/0166-6851(81)90011-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We have compared a total of 44 recognition sites for 12 restriction endonucleases on the 20 kilobase pair maxi-circle of kinetoplast DNA from nine Trypanosoma brucei stocks, four which are known to be infective to man (tow 'gambiense' and two 'rhodesiense' variants). In addition to five polymorphic sites, these DNAs differ in the size of a 5 kilo-base pair region which is cleaved only by one of the restriction enzymes tested and which varies in size over 1.5 kilo-base pairs. Our analysis shows that the maxi-circle sequences of these stocks are very similar, the maximal calculated difference between any two being 3%. A relatively large difference was found between a rhodesiense stock from uganda and one from Zambia, confirming the distinction between northern and southern East African rhodesiense stocks found by analysis of enzyme polymorphisms (Gibson et al. (1980) Adv. Parasitol. 18, 175-246). The gambiense variants could not be identified by unique restriction site polymorphisms, but contained the smallest maxi-circle found thus far in T. Brucei. Our results indicate that T. brucei stocks infective and not infective to man are so closely related as to preclude their differentiation by analysis of kinetoplast DNA. This analysis is useful, however, in providing quantitative information about relatedness of stocks.
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Hoeijmakers JH, Snijders A, Janssen JW, Borst P. Transcription of kinetoplast DNA in Trypanosoma brucei bloodstream and culture forms. Plasmid 1981; 5:329-50. [PMID: 6267635 DOI: 10.1016/0147-619x(81)90009-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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21
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Stahly DP, Ito J. Transfection of protoplasts of Bacillus subtilis with phi 29 DNA. MOLECULAR & GENERAL GENETICS : MGG 1981; 182:180-2. [PMID: 6790910 DOI: 10.1007/bf00422788] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Yoshikawa H, Ito J. Terminal proteins and short inverted terminal repeats of the small Bacillus bacteriophage genomes. Proc Natl Acad Sci U S A 1981; 78:2596-600. [PMID: 6941313 PMCID: PMC319396 DOI: 10.1073/pnas.78.4.2596] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The genome of Bacillus phage phi 29 contains covalently linked protein at both ends. These DNA terminal proteins are essential for phi 29 DNA replication. We have isolated phi 29 terminal protein from each end separately and compared their two-dimensional peptide maps. Our results showed the two proteins to be identical. The DNAs of four phages examined (phi 15, Nf, M2Y, and GA-1) also contain protein at both ends of the DNA molecules. The chymotryptic peptide maps of these DNA terminal proteins have been compared with the map of the phi 29 terminal protein. Despite the similarities in molecular size, peptide maps of the terminal proteins show clear differences among the unrelated phages. These results are consistent with the idea that the terminal proteins are encoded by viral DNA rather than by the host chromosome. We have also determined the nucleotide sequences of the termini of four phage DNAs and compared them with the sequence of phi 29 DNA. The sequence data indicate that all of these phages DNA contain short inverted terminal repeats: 5'A-A-A-G-T-A for phi 29 and phi 15, 5' A-A-A-G-T-A-A-G for Nf and M2Y, and 5' A-A-A-T-A-G-A for GA-1.
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23
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Yoshikawa H, Friedmann T, Ito J. Nucleotide sequences at the termini of phi 29 DNA. Proc Natl Acad Sci U S A 1981; 78:1336-40. [PMID: 6262789 PMCID: PMC319125 DOI: 10.1073/pnas.78.3.1336] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequences of the first 422 base pairs from the left-hand end and the first 274 base pairs from the right-hand end of phi 29 DNA were determined by using the chemical degradation method of Maxam and Gilbert. The data indicate that phi 29 DNA has inverted terminal repetitions that are six base pairs long 5' (-A-A-A-G-T-A-). No perfectly self-complementary sequence exists within the terminal regions of phi 29 DNA, suggesting that DNA replication via a self-priming mechanism is improbable. The putative early promoter sequences were found in both ends of the phi 29 DNA. The results of the sequence determination are discussed in relation ship to models proposed for the mechanism of replication of linear DNA molecules.
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24
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Slinker BS, Burke WF. Isolation and characterization of a manganese-stimulated exonuclease fromBacillus subtilis. Curr Microbiol 1981. [DOI: 10.1007/bf01566592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Borst P, Fase-Fowler F, Hoeijmakers JH, Frasch AC. Variations in maxi-circle and mini-circle sequences in kinetoplast DNAs from different Trypanosoma brucei strains. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 610:197-210. [PMID: 6260147 DOI: 10.1016/0005-2787(80)90001-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have compared a total of 30 recognition sites for eight restriction endonucleases on the 20-kilobase-pair maxi-circle of kinetoplast DNAs from five different Trypanosoma brucei strains. In addition to three polymorphic sites were have found a 5 kilobase-pair region that is not cleaved by any of the eight enzymes and that varies in size over 1 kilobase pair in the strains analysed. Mini-circles from these five strains, digested with endonuclease TaqI or MboII, yield very complex fragment patterns, showing that extensive mini-circle sequence heterogeneity is a common characteristic of these T. brucei strains. The size distribution of mini-circle fragments in these digests was identical for different clones of the 427 strain, but very different for mini-circles from different strains. These results show that maxi-circle sequence is conserved, whereas mini-circle sequence is not. Restriction digests of maxi-circles could be useful in determining how closely two Trypanosoma strains are related, whereas mini-circle digests can serve as sensitive tags for individual strains.
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26
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Kawamura F, Saito H, Ikeda Y. Bacteriophage phi 1 as a gene-cloning vector in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1980; 180:259-66. [PMID: 6258022 DOI: 10.1007/bf00425837] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We attempted to use Bacillus subtilis phage phi 1 as a gene-cloning vector since the phi 1 genome was found to have few cleavage sites upon digestion with several kinds of restriction endonucleases. A phi 1 stock supplied by J. Ito (University of Arizona, Tucson, USA) consisted of two phages, phi 1E1 and phi 1E2, having one and two EcoRI-cleavage sites in their genomes respectively. From the latter isolate a deletion mutant phi 1E2 delta 1 was induced to increase the size range of DNA segments to be cloned. It was demonstrated, by in vitro recombination experiments with phage rho 11 DNA, that phi 1E2 delta 1 can be used for cloning EcoRI fragments of various sizes. We analyzed the DNAs of ten phi 1 clones isolated from independent transfectants and found that six of them carried rho 11 DNA fragments inserted at either of the two EcoRI-cleavage sites. Some of the hybrid phage DNAs were found to be cleaved with BamHI and HaeIII endonucleases and the rho 11 DNA portion, whereas the parental phi 1E2 delta 1 DNA was insensitive to any of these enzymes. These hybrid phages would therefore be useful vectors for cloning foreign DNA fragments generated by cleavage with BamHI or HaeIII endonucleases.
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27
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Mizukami T, Kawamura F, Takahashi H, Saito H. A physical map of the genome of the Bacillus subtilis temperate phage rho 11. Gene 1980; 11:157-62. [PMID: 6254851 DOI: 10.1016/0378-1119(80)90095-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A cleavage map of Bacillus subtilis temperate phage rho 11 was constructed with restriction endonucleases SalI, BamHI and BglII, which cut the genome into 6, 7 and 21 fragments, respectively. The molecular weight of the rho 11 genome was calculated to be 78 x 10(6). Among other endonucleases tested, PvuII, EcoRI and XbaI cleaved the genome into more than 25 fragments, while HaeIII, StuI, BalI and BamNx did not cut the genome at all. The rho 11-coded thymidylate synthetase gene, thyP11, was found to be located in the SalI-D fragment, which was in the central region of the genome.
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Davison B, Murray C, Rabinowitz J. Specificity of promoter site utilization in vitro by bacterial RNA polymerases on Bacillus phage phi 29 DNA. Transcription mapping with exonuclease III. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(18)43576-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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29
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Dickel CD, Burtis KC, Doi RH. Delta factor increases promoter selectivity of Bacillus subtilis vegetative cell RNA polymerase. Biochem Biophys Res Commun 1980; 95:1789-95. [PMID: 6158327 DOI: 10.1016/s0006-291x(80)80106-9] [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: 01/18/2023]
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Harding NE, Ito J. DNA replication of bacteriophage phi 29: characterization of the intermediates and location of the termini of replication. Virology 1980; 104:323-38. [PMID: 7395108 DOI: 10.1016/0042-6822(80)90337-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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31
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Iijima T, Kawamura F, Saito H, Ikeda Y. A specialized transducing phage constructed from Bacillus subtilis phage phi 105. Gene X 1980; 9:115-26. [PMID: 6769751 DOI: 10.1016/0378-1119(80)90170-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Chromosomal DNA of Bacillus subtilis 168 (trpC2) prepared from defective phage P BSX was digested by restriction endonuclease Eco RI and ligated in vitro with DNA fragments of page phi 105C digested by the same endonuclease. The ligated DNA was used to transform a competent culture of B. subtilis (trpC2 lys3 metB10) which was lysogenic for phi 105, and transformants of the auxotroph markers were selected. The bacterial DNA ligated to the phage DNA fragments could be integrated into the prophage genome by transformation. The transformants in toto were treated with mitomycin C and the lysate was used to transduce B. subtilis (trpC2 lys3 metB10). Among metB+ transductants, one clone appeared to be a double lysogen carrying both plaque forming and metB+ transducing phage genomes. The latter defective phage was designated phi 105dmetB. Physical mapping of these phages was carried out by agarose gel electrophoresis of the restriction endonuclease digests and also by electron microscopic analysis of heteroduplex DNA. These results indicate that two adjacent fragments Eco RI-G and E of phi 105 DNA had been substituted with a foreign fragment Eco RI-M in phi 105dmetB DNA. Transformation experiments showed that the metB+ gene resided on the fragment Eco RI-M. This fragment was found to have a BamHI-sensitive site. The transforming activity for the metB marker, however, was not affected by the treatmment with BamHI.
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32
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Borst P, Fase-Fowler F, Frasch A, Hoeijmakers J, Weijers P. Characterization of DNA from Trypanosoma brucei and related trypanosomes by restriction endonuclease digestion. Mol Biochem Parasitol 1980. [DOI: 10.1016/0166-6851(80)90030-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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33
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Borst P, Fase-Fowler F. The maxi-circle of Trypanosoma brucei kinetoplast DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 565:1-12. [PMID: 508755 DOI: 10.1016/0005-2787(79)90078-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have constructed a fragment map of the maxi-circle component from kinetoplast DNA networks of Trypanosoma brucei brucei (East African Trypanosomiasis Research Organization strain No. 427), using restriction endonucleases PstI, HapII, EcoRI, BglI, HindIII, HhaI, SstI, XbaI, HaeIII and Sau-96I. Although the 20 kilo-base pair map contains 30 fragments, there is a 6.5 kilo-base pair 'silent' segment which lacks recognition sites for any of these enzymes. In CsCl intact kinetoplast DNA has a buoyant density of 1.690 g/cm3, whereas a kinetoplast DNA fraction enriched in maxi-circle sequences contains an additional component at 1.682 g/cm3. The possibility that the 'silent' segment is very rich in A + T is discussed.
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34
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Davison B, Leighton T, Rabinowitz J. Purification of Bacillus subtilis RNA polymerase with heparin-agarose. In vitro transcription of phi 29 DNA. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86833-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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35
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Yoneda Y, Graham S, Young FE. Restriction-fragment map of the temperate Bacillus subtilis bacteriophage SPO2. Gene 1979; 7:51-68. [PMID: 115752 DOI: 10.1016/0378-1119(79)90042-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The endonucleases BglI, BglII, EcoRI, SalI, SmaI, and XbaI were used to fragment the phage SPO2 DNA. Electrophoretic analysis using ethidiumbromide agarose gels showed the phage to have nine BglI sites, one BglII site, four EcoRI sites, one SalI site, one SmaI site, and six XbaI sites. Using partial digestions, multiple endonuclease digestion, and autoradiography the fragments were sized and ordered into a circular map of 23 Md. Such an analysis locates the endonuclease sites, indicates which endonucleases are potentially useful in cloning with SPO2, and allows insertions and/or deletions in the SPO2 DNA to be characterized.
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36
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Abstract
A physical map of the genome of Bacillus subtilis bacteriophage phi 3T was constructed by ordering the fragments produced by cleavage of phi 3T DNA with restriction endonucleases AvaII (2 fragments), BglI (2 fragments), SmaI (3 fragments), BamHI (6 fragments), SalI (7 fragments), AvaI (7 fragments), SacI (12 fragments), PstI (14 fragments), and BglII (26 fragments). Two techniques were used to order the fragments: (1) Sets of previously ordered restriction fragments were isolated and redigested with the endonuclease whose cleavage sites were to be mapped. (2) Fragments located near the ends of the genome or near the ends of other restriction fragments were ordered by treating the DNA with lambda exonuclease prior to restriction endonuclease cleavage. The susceptibility of phi 3T DNA to 15 other restriction endonucleases is also reported.
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37
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Faust RM, Spizizen J, Gage V, Travers RS. Extrachromosomal DNA in Bacillus thuringiensis var. kurstaki, var. finitimus, var. sotto, and in Bacillus popilliae. J Invertebr Pathol 1979. [DOI: 10.1016/0022-2011(79)90158-7] [Citation(s) in RCA: 9] [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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38
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Abstract
Susceptibility of Bacillus subtilis phage phi 29 DNA to 34 different restriction endoculceases was determined. Three enzymes, BglI, XbaI and BstEII, were found to cleave phi 29 DNA only once at specific sites. The sites of these single cleavages have been mapped. Thirteen enzymes did not cut phi 29 DNA. phi 29 HindIII DNA fragments inserted into pBR313 plasmid and propagated in Escherichia coli, were resistant to these restriction endonucleases. This result suggests that the insusceptibility is due to the absence of the nucleotide sequences on phi 29 recognized by the enzymes, and not to the presence of modified nucleotides.
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39
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Thomas C, Saigo K, McLeod E, Ito J. The separation of DNA segments attached to proteins. Anal Biochem 1979. [DOI: 10.1016/s0003-2697(79)80130-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Ito J. Bacteriophage phi29 terminal protein: its association with the 5' termini of the phi29 genome. J Virol 1978; 28:895-904. [PMID: 731797 PMCID: PMC525814 DOI: 10.1128/jvi.28.3.895-904.1978] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The location of the protein bound to bacteriophage phi29 DNA has been studied with restriction endonucleases, exonucleases, and polynucleotide kinase. The protein is invariably associated with the two terminal DNA fragments generated by restriction endonucleases. The phi29 DNA prepared with or without proteinase K treatment is resistant to the action of the 5'-terminal-specific exonucleases, lambda-exonuclease and T7 exonuclease. The phi29 DNA is also inaccessible to phosphorylation by polynucleotide kinase even after treatment with alkaline phosphatase. On the other hand, phi29 DNA is sensitive to exonuclease III, and the 3' termini of the DNA can be labeled by incubating with alpha-[32P]ATP and terminal deoxynucleotidyl transferase. The protein remains associated with the phi29 DNA after treatment with various chaotropic agents, including 8 M urea, 6 M guanidine-hydrochloride, 4 M sodium perchlorate, 2 M sodium thiocyanate, and 2 M LiCl. These results are consistent with the notion that the protein is linked covalently to the 5' termini of the phi29 DNA.
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41
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Mastromei G, Riva S. SPP1 DNA replicative forms: growth of phage SPP1 in Bacillus subtilis mutants temperature-sensitive in DNA synthesis. MOLECULAR & GENERAL GENETICS : MGG 1978; 167:157-64. [PMID: 104141 DOI: 10.1007/bf00266909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The development of bacteriophages SPP1 and phi 29 has been studied in several B. sutilis mutants defective in host DNA replication, under non permissive conditions. Several gene products, involved in the synthesis of host DNA, are required for phi 29 replication, while SPP1 seems to require only the host DNA polymerase III. In addition both phages are unable to grow in a dna A mutant (ribonucleotide reductase). Taking advantage of the fact that SPP1 DNA is actively replicated in several dna mutants at non-permissive temperature, we have studied the structure of the replicative intermediates of this phage in the absence of interfering host DNA synthesis. Fast sedimenting forms of SPP1 DNA can be isolated from phage infected cells and evidence of covalently joined concatemers has been obtained, suggesting the presence of terminally repeated sequences.
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42
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Goldbach RW, Borst P, Bollen-de Boer JE, van Bruggen EF. The organization of ribosomal RNA genes in the mitochondrial DNA of Tetrahymena pyriformis strain ST. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 521:169-86. [PMID: 102353 DOI: 10.1016/0005-2787(78)90260-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1. We have constructed a physical map of the mtDNA of Tetrahymena pyriformis strain ST using the restriction endonucleases EcoRI, PstI, SacI, HindIII and HhaI. 2. Hybridization of mitochondrial 21 S and 14 S ribosomal RNA to restriction fragments of strain ST mtDNA shows that this DNA contains two 21-S and only one 14-S ribosomal RNA genes. By S1 nuclease treatment of briefly renatured single-stranded DNA the terminal duplication-inversion previously detected in this DNA (Arnberg et al. (1975) Biochim. Biophys. Acta 383, 359--369) has been isolated and shown to contain both 21-S ribosomal RNA genes. 14 S ribosomal RNA hybridizes to a region in the central part of the DNA, about 8000 nucleotides or 20% of the total DNA length apart from the nearest 21 S ribosomal RNA gene. 3. We have confirmed this position of the three ribosomal RNA genes by electron microscopical analysis of DNA . RNA hybrid molecules and R-loop molecules. 4. Hybridization of 21 S ribosomal RNA with duplex mtDNA digested either with phage lambda-induced exonuclease or exonuclease III of Escherichia coli, shows that the 21-S ribosomal RNA genes are located on the 5'-ends of each DNA strand. Electron microscopy of denaturated mtDNA hybridized with a mixture of 14-S and 21-S ribosomal RNAs show that the 14 S ribosomal RNA gene has the same polarity as the nearest 21 S ribosomal RNA gene. 5. Tetrahymena mtDNA is (after Saccharomyces mtDNA) the second mtDNA in which the two ribosomal RNA cistrons are far apart and the first mtDNA in which one of the ribosomal RNA cistrons is duplicated.
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van den Berg J, van Ooyen A, Mantei N, Schamböck A, Grosveld G, Flavell RA, Weissmann C. Comparison of cloned rabbit and mouse beta-globin genes showing strong evolutionary divergence of two homologous pairs of introns. Nature 1978; 276:37-44. [PMID: 264241 DOI: 10.1038/276037a0] [Citation(s) in RCA: 136] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cloned beta-globin genes of both mouse and rabbit each contain a large and a small intervening sequence (intron) of about equal length at precisely the same positions relative to the coding sequence. The homologous introns show some sequence similarity, particularly at the junctions with the coding sequence. They most probably arose from a common ancestral sequence and diverged substantially during evolution.
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44
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Taniguchi T, Palmieri M, Weissmann C. QB DNA-containing hybrid plasmids giving rise to QB phage formation in the bacterial host. Nature 1978; 274:223-8. [PMID: 355887 DOI: 10.1038/274223a0] [Citation(s) in RCA: 130] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hybrid plasmids consisting of PCRI and a complete DNA copy of the RNA genome of coli.phage QB, inserted in either orientation, elicit the formation of phage QB when introduced into Escherichia coli
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45
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Farrell R, Gunsalus IC, Crawford IP, Johnston JB, Ito J. Restriction endonuclease sites and aromatic metabolic plasmid structure. Biochem Biophys Res Commun 1978; 82:411-6. [PMID: 666852 DOI: 10.1016/0006-291x(78)90891-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Salas M, Mellado RP, Viñuela E. Characterization of a protein covalently linked to the 5' termini of the DNA of Bacillus subtilis phage phi29. J Mol Biol 1978; 119:269-91. [PMID: 416224 DOI: 10.1016/0022-2836(78)90438-2] [Citation(s) in RCA: 170] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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47
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Harding NE, Ito J, David GS. Identification of the protein firmly bound to the ends of bacteriophage phi 29 DNA. Virology 1978; 84:279-92. [PMID: 203093 DOI: 10.1016/0042-6822(78)90248-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Fairlamb AH, Weislogel PO, Hoeijmakers JH, Borst P. Isolation and characterization of kinetoplast DNA from bloodstream form of Trypanosoma brucei. J Cell Biol 1978; 76:293-309. [PMID: 10605439 PMCID: PMC2109978 DOI: 10.1083/jcb.76.2.293] [Citation(s) in RCA: 124] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have used restriction endonucleases PstI, EcoRI, HapII, HhaI, and S1 nuclease to demonstrate the presence of a large complex component, the maxi-circle, in addition to the major mini-circle component in kinetoplast DNA (kDNA) networks of Trypanosoma brucei (East African Trypanosomiasis Research Organization [EATRO] 427). Endonuclease PstI and S1 nuclease cut the maxi-circle at a single site, allowing its isolation in a linear form with a mol wt of 12.2 x 10(6), determined by electron microscopy. The other enzymes give multiple maxi-circle fragments, whose added mol wt is 12-13 x 10(6), determined by gel electrophoresis. The maxi-circle in another T. brucei isolate (EATRO 1125) yields similar fragments but appears to contain a deletion of about 0.7 x 10(6) daltons. Electron microscopy of kDNA shows the presence of DNA considerably longer than the mini-circle contour length (0.3 micron) either in the network or as loops extending from the edge. This long DNA never exceeds the maxi-circle length (6.3 microns) and is completely removed by digestion with endonuclease PstI. 5-10% of the networks are doublets with up to 40 loops of DNA clustered between the two halves of the mini-circle network and probably represent a division stage of the kDNA. Digestion with PstI selectively removes these loops without markedly altering the mini-circle network. We conclude that the long DNA in both single and double networks represents maxi-circles and that long tandemly repeated oligomers of mini-circles are (virtually) absent. kDNA from Trypanosoma equiperdum, a trypanosome species incapable of synthesizing a fully functional mitochondrion, contains single and double networks of dimensions similar to those from T. brucei but without any DNA longer than mini-circle contour length. We conclude that the maxi-circle of trypanosomes is the genetic equivalent of the mitochondrial DNA (mtDNA) of other organisms.
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Affiliation(s)
- A H Fairlamb
- Section for Medical Enzymology and Molecular Biology, University of Amsterdam, The Netherlands
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Koutecká E, Černá E, Neubauer Z, Doskočil J. Phase variation concerning the regulation of phage expression in non-defective λ lysogens: The involvement of prophage-derived plasmids and of the shifts in their oligomerisation. ACTA ACUST UNITED AC 1978. [DOI: 10.1007/bf00267203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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