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Tridgett M, Ababi M, Jaramillo A. Lambda Red Recombineering of Bacteriophage in the Lysogenic State. Methods Mol Biol 2022; 2479:11-19. [PMID: 35583729 DOI: 10.1007/978-1-0716-2233-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present a recombineering-based method for editing the genome of a temperate phage. The method uses the lambda Red recombination system to edit the genome of a lysogenized host with a prophage compatible with bacteriophage lambda. Linear DNA is used as the recombination substrate and antibiotic resistance is used as the basis for selection of recombinants. The method enables the genetic manipulation of a prophage in 3-5 days.
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Affiliation(s)
| | - Maria Ababi
- School of Life Sciences, University of Warwick, Coventry, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Alfonso Jaramillo
- School of Life Sciences, University of Warwick, Coventry, UK.
- De novo Synthetic Biology Lab, I2SysBio, CSIC-University of Valencia, Paterna, Spain.
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2
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Tridgett M, Ababi M, Osgerby A, Ramirez Garcia R, Jaramillo A. Engineering Bacteria to Produce Pure Phage-like Particles for Gene Delivery. ACS Synth Biol 2021; 10:107-114. [PMID: 33317264 DOI: 10.1021/acssynbio.0c00467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Natural and engineered phages have been used in many applications, but their use to deliver user-defined genetic cargoes has been hampered by contamination with replicative phage, restricting use of the technology beyond the laboratory. Here we present a method to produce transducing particles without contamination. In addition, we demonstrate the use of a helper phage-free transducing particle preparation as an antimicrobial agent. This will pave the way for the development of new phage-based technologies with greater scope than lytic phage therapy.
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Affiliation(s)
- Matthew Tridgett
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Maria Ababi
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alexander Osgerby
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Robert Ramirez Garcia
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
- CNRS, Paris, 75016, France
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3
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Chattoraj DK, Younghusband HB, Inman RB. Physical mapping of bacteriophage P2 mutations and their relation to the genetic map. ACTA ACUST UNITED AC 2005; 136:139-49. [PMID: 16094980 DOI: 10.1007/bf00272035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three new deletion mutants and an insertion mutant of E. coli bacteriophage P2, del2, vir79, del4 and sig5, were mapped by the electron microscope heteroduplex method. The deletions were found to cover 45.5-51.6%, 75.6-76.7% and 92.3-99.3% respectively of P2 DNA while sig5 represented a 3.7% insertion at 78.6% from the left end. The region covering 75.9-76.7% of P2 DNA is also deleted in the two previously characterized immunity insensitive variants of P2, vir22 and Hy dis. This region may identify the portion of the genome responsible for immunity. The physical and genetic maps of P2 were previously found to be colinear with respect to the two mutations vir22 and vir37. This relationship is confirmed by the position of del2.
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Affiliation(s)
- D K Chattoraj
- Biophysics Laboratory and Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, USA
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4
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Affiliation(s)
- Giuseppe Bertani
- Biology Division, California Institute of Technology, Pasadena, California 91125, USA.
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5
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Bertani G. Transduction-like gene transfer in the methanogen Methanococcus voltae. J Bacteriol 1999; 181:2992-3002. [PMID: 10321998 PMCID: PMC93752 DOI: 10.1128/jb.181.10.2992-3002.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/1998] [Accepted: 03/01/1999] [Indexed: 11/20/2022] Open
Abstract
Strain PS of Methanococcus voltae (a methanogenic, anaerobic archaebacterium) was shown to generate spontaneously 4.4-kbp chromosomal DNA fragments that are fully protected from DNase and that, upon contact with a cell, transform it genetically. This activity, here called VTA (voltae transfer agent), affects all markers tested: three different auxotrophies (histidine, purine, and cobalamin) and resistance to BES (2-bromoethanesulfonate, an inhibitor of methanogenesis). VTA was most effectively prepared by culture filtration. This process disrupted a fraction of the M. voltae cells (which have only an S-layer covering their cytoplasmic membrane). VTA was rapidly inactivated upon storage. VTA particles were present in cultures at concentrations of approximately two per cell. Gene transfer activity varied from a minimum of 2 x 10(-5) (BES resistance) to a maximum of 10(-3) (histidine independence) per donor cell. Very little VTA was found free in culture supernatants. The phenomenon is functionally similar to generalized transduction, but there is no evidence, for the time being, of intrinsically viral (i.e., containing a complete viral genome) particles. Consideration of VTA DNA size makes the existence of such viral particles unlikely. If they exist, they must be relatively few in number;perhaps they differ from VTA particles in size and other properties and thus escaped detection. Digestion of VTA DNA with the AluI restriction enzyme suggests that it is a random sample of the bacterial DNA, except for a 0.9-kbp sequence which is amplified relative to the rest of the bacterial chromosome. A VTA-sized DNA fraction was demonstrated in a few other isolates of M. voltae.
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Affiliation(s)
- G Bertani
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA.
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6
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Piazza F, Zappone M, Sana M, Briani F, Dehò G. Polynucleotide phosphorylase of Escherichia coli is required for the establishment of bacteriophage P4 immunity. J Bacteriol 1996; 178:5513-21. [PMID: 8808944 PMCID: PMC178376 DOI: 10.1128/jb.178.18.5513-5521.1996] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bacteriophage P4's superinfection immunity mechanism is unique among those of other known bacteriophages in several respects: (i) the P4 immunity factor is not a protein but a short, stable RNA (CI RNA); (ii) in the prophage the expression of the replication operon is prevented by premature transcription termination rather than by repression of transcription initiation; (iii) transcription termination is controlled via RNA-RNA interactions between the CI RNA and two complementary target sequences on the nascent transcript; and (iv) the CI RNA is produced by processing of the same transcript it controls. It was thought that several host-encoded factors may participate in the molecular events required for P4 immunity expression, i.e., RNA processing, RNA-RNA interactions, and transcription termination. To identify such factors we searched for Escherichia coli mutations that affect P4 lysogenization. One such mutation, bfl-1, severely reduced P4's lysogenization frequency and delayed both the disappearance of the long transcripts that cover the entire replication operon and the appearance of the CI RNA. By physical mapping and genetic analysis we show that bfl-1 is allelic to pnp, which codes for polynucleotide phosphorylase, a 3'-to-5' exonucleolytic enzyme. A previously isolated pnp null mutant (pnp-7) exhibited a phenotype similar to that of bfl-1. These results indicate that the polynucleotide phosphorylase of E. coli is involved with the maturation pathway of bacteriophage P4's RNA immunity factor.
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Affiliation(s)
- F Piazza
- Dipartimento di Genetica e di Biologia dei Microorganismi, Università degli Studi di Milano, Italy
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7
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Isaksen ML, Rishovd ST, Calendar R, Lindqvist BH. The polarity suppression factor of bacteriophage P4 is also a decoration protein of the P4 capsid. Virology 1992; 188:831-9. [PMID: 1585650 DOI: 10.1016/0042-6822(92)90538-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We show that the product of the polarity suppression (psu) gene from bacteriophage P4 associates with P4 capsids. This association can occur when Psu is (i) provided in vivo from the P4 genome or from a plasmid or (ii) provided in vitro by mixing viable phage particles with Psu protein. Psu is unable to associate with the larger capsid of P4's helper phage P2. Discrimination of the P4 and P2 capsids by Psu appears to be independent of the presence of the P4 genome in the capsid, since P2 size capsids filled with P4 DNA cannot accommodate Psu association. P4 psu particles devoid of Psu are less stable than P4 particles carrying Psu. These results indicate that, in addition to its antitermination activity at Rho-dependent terminators, Psu is also a decoration protein that stabilizes the P4 capsids.
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Affiliation(s)
- M L Isaksen
- Institute of Biology, University of Oslo, Norway
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8
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Haggård-Ljungquist E, Halling C, Calendar R. DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. J Bacteriol 1992; 174:1462-77. [PMID: 1531648 PMCID: PMC206541 DOI: 10.1128/jb.174.5.1462-1477.1992] [Citation(s) in RCA: 154] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have determined the DNA sequence of the bacteriophage P2 tail genes G and H, which code for polypeptides of 175 and 669 residues, respectively. Gene H probably codes for the distal part of the P2 tail fiber, since the deduced sequence of its product contains regions similar to tail fiber proteins from phages Mu, P1, lambda, K3, and T2. The similarities of the carboxy-terminal portions of the P2, Mu, ann P1 tail fiber proteins may explain the observation that these phages in general have the same host range. The P2 H gene product is similar to the products of both lambda open reading frame (ORF) 401 (stf, side tail fiber) and its downstream ORF, ORF 314. If 1 bp is inserted near the end of ORF 401, this reading frame becomes fused with ORF 314, creating an ORF that may represent the complete stf gene that encodes a 774-amino-acid-long side tail fiber protein. Thus, a frameshift mutation seems to be present in the common laboratory strain of lambda. Gene G of P2 probably codes for a protein required for assembly of the tail fibers of the virion. The entire G gene product is very similar to the products of genes U and U' of phage Mu; a region of these proteins is also found in the tail fiber assembly proteins of phages TuIa, TuIb, T4, and lambda. The similarities in the tail fiber genes of phages of different families provide evidence that illegitimate recombination occurs at previously unappreciated levels and that phages are taking advantage of the gene pool available to them to alter their host ranges under selective pressures.
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Halling C, Sunshine MG, Lane KB, Six EW, Calendar R. A mutation of the transactivation gene of satellite bacteriophage P4 that suppresses the rpoA109 mutation of Escherichia coli. J Bacteriol 1990; 172:3541-8. [PMID: 2193910 PMCID: PMC213326 DOI: 10.1128/jb.172.7.3541-3548.1990] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Satellite bacteriophage P4 requires the products of the late genes of a helper such as P2 in order to grow lytically. The Escherichia coli rpoA109 mutation, which alters the alpha subunit of RNA polymerase, prevents transcription of the late genes of bacteriophage P2. Suppressor mutations that define the P2 ogr gene overcome this block. We found that P4 lytic growth using a P2 ogr+ prophage helper was prevented by the rpoA109 mutation but that this block was overcome when the P2 helper carried the suppressor mutation in the ogr gene. Furthermore, we isolated and characterized four independent mutations in P4, called org, that suppress the E. coli rpoA109 mutation by allowing P4 lytic growth using a P2 ogr+ helper. DNA sequence analysis revealed that the four independent org mutations are identical and that they occur in the P4 delta gene, which codes for a factor that positively regulates the transcription of the P2 and P4 late genes. delta is predicted to code for a basic 166-amino-acid residue protein. Each 83-residue half of the predicted delta gene product is similar to the predicted 72-residue proteins encoded by the ogr gene of P2 and the B gene of phage 186.
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Affiliation(s)
- C Halling
- Department of Molecular Biology, University of California, Berkeley 94720
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10
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Birkeland NK, Lindquist BH. Coliphage P2 late control gene ogr. DNA sequence and product identification. J Mol Biol 1986; 188:487-90. [PMID: 3735430 DOI: 10.1016/0022-2836(86)90170-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The bacteriophage P2 late control gene ogr was cloned and precisely localized by deletion analysis in vitro. The DNA sequence of the ogr gene containing the ogr1 mutation was determined. The sequence translates into a basic protein of a molecular weight of 8300. Plasmids overproducing the ogr gene product were constructed, and the ogr gene product was identified by polyacrylamide gel electrophoresis.
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Schnös M, Inman RB. Reinitiation during lambda DNA replication resulting from either cis-Pt treatment or infection of a P2 lysogenic strain. Virology 1985; 145:304-12. [PMID: 3161238 DOI: 10.1016/0042-6822(85)90163-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nested areas of replication are observed in phage lambda replicative intermediates and arise from reinitiation from the lambda origin. Reinitiation occurs when the first round of lambda replication takes place in the presence of the drug cis-Pt or when lambda infects a host which has been preincubated with the drug. In the latter case it is shown that the infection proceeds during the expression of SOS functions induced in the host as a result of the drug treatment. When lambda infects a host lysogenic for phage P2, an interference process occurs which prevents formation of lambda phage. The lambda DNA does, however, undergo at least one round of replication but is abnormal in that lambda origins reinitiate to form nested areas of replication similar to those resulting from exposure to the drug cis-Pt.
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12
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Lundqvist B, Bertani G. Immunity repressor of bacteriophage P2. Identification and DNA-binding activity. J Mol Biol 1984; 178:629-51. [PMID: 6492160 DOI: 10.1016/0022-2836(84)90242-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The product of gene C of the temperate bacteriophage P2, the immunity repressor, can be detected as a unique band eluting from phosphocellulose columns at 0.12 M-potassium phosphate when differentially labelled with a radioactive amino acid: the band is absent when phages that either have lost gene C through deletion or carry a suppressor-sensitive mutation in the gene are used. The repressor in its monomeric form is about 11,000 in molecular weight. At near physiological salt concentrations, the form predominantly recovered is the dimer. In filter-binding assays, the partially purified repressor binds wild-type P2 DNA strongly. It does not bind DNA of P2 vir94, a deletion that removes all the genetic elements involved in the regulation of lysogeny; it also does not bind, or binds inefficiently, DNA of P2 vir3, a mutation in the operator that controls the early replicative functions of P2. At the concentrations employed, the dimer is the active form in binding. The P2 repressor clearly differs in several features from the well-studied immunity repressor of bacteriophage lambda.
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13
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Ljungquist E, Kockum K, Bertani LE. DNA sequences of the repressor gene and operator region of bacteriophage P2. Proc Natl Acad Sci U S A 1984; 81:3988-92. [PMID: 6330728 PMCID: PMC345353 DOI: 10.1073/pnas.81.13.3988] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nucleotide sequence of the repressor gene C of the temperate phage P2 has been determined. It codes for a nonbasic polypeptide, 99 amino acids long. Twelve repressor-defective mutants have been mapped. All but one are located within the presumed coding part of the gene. There is a strong promoter sequence and an 8-base-pair inverted repeat preceding the gene. The P2 repressor protein shows structural similarity to other DNA-binding proteins. The operator region for the early replication functions was located by sequencing the DNA of three virulent mutants. The sequence indicates that there are two repressor-binding sites. In addition, one of the sites shows sequence homology with part of the operator region of the biotin operon of Escherichia coli.
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14
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Abstract
Glutamine synthetase is a major enzyme in the assimilation of ammonia by members of the genus Rhizobium. Two forms of glutamine synthetase are found in members of the genus Rhizobium, a heat-stable glutamine synthetase I (GSI) and a heat-labile GSII. As a step toward clarifying the role of these enzymes in symbiotic nitrogen fixation, we have cloned the structural gene for GSI from Rhizobium meliloti 104A14. A gene bank of R. meliloti was constructed by using the bacteriophage P4 cosmid pMK318. Cosmids that contain the structural gene for GSI were isolated by selecting for plasmids that permit ET8051, an Escherichia coli glutamine autotroph, to grow with ammonia as the sole nitrogen source. One of the cosmids, pJS36, contains an insert of 11.9 kilobases. ET8051(pJS36) grows slowly on minimal media. When a 3.7-kilobase HindIII fragment derived from this DNA is cloned into the HindIII site of pACYC177 and the plasmids are transformed into ET8051, rapid growth is observed when the insert is in one orientation (pJS44) but not the other (pJS45). Glutamine synthetase activity can be detected in ET8051(pJS44); most of this activity is heat stable. pJS36 hybridizes with the glnA structural gene from Escherichia coli. Insertion of a 2.7-kilobase Tetr determinant into a BglII site located within pJS44 abolishes all glutamine synthetase activity. This interrupted version of a glutamine synthetase gene was substituted for the normal R. meliloti sequence by homologous recombination in R. meliloti. Recombinants lose GSI activity, but retain GSII activity and grow well with ammonia as the sole nitrogen source. These mutants are unaffected in nodulation and nitrogen fixation.
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15
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Ljungquist E, Bertani LE. Properties and products of the cloned int gene of bacteriophage P2. MOLECULAR & GENERAL GENETICS : MGG 1983; 192:87-94. [PMID: 6358802 DOI: 10.1007/bf00327651] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fragments of DNA of the temperate phage P2, generated by treatment with the restriction enzyme PstI, have been cloned into the plasmid pBR322. One such fragment, which has its endpoints within phage genes T and C, carries the structural P2 int gene as well as its promoter and the phage att site. When introduced into a suitable bacterial host, the cloned fragment mediates the integration and excision of int- mutants of P2 and recombination within the phage att site in mixed infection. All these activities are independent of the orientation of the fragment within the plasmid. When introduced into minicells, the fragment produces, in addition to the products of genes D and U, a protein of 35-37,000 daltons identified as the int protein. A study of the map location of two amber int mutants, together with the sizes of the polypeptides they produce, indicates that the P2 int gene is transcribed from right to left on the P2 map, i.e. starting near gene C and proceeding toward att.
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16
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Gibbs W, Eisen H, Calendar R. In vitro activation of bacteriophage P2 late gene expression by extracts from phage P4-infected cells. J Virol 1983; 47:392-8. [PMID: 6620459 PMCID: PMC255279 DOI: 10.1128/jvi.47.3.392-398.1983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We have used a cell-free, DNA-dependent protein-synthesizing system to study the stimulation of phage P2 late gene expression by satellite phage P4. An activity is present in extracts prepared from P4-infected cells, which, when added to the in vitro system with P2 DNA template, stimulates the synthesis of a number of P2 proteins. These stimulated proteins include the major P2 capsid protein (N gene product) and a major component of the P2 phage tail (FII gene product). Extracts prepared from P4-infected cells are also able to stimulate the synthesis from P4 DNA of two low-molecular-weight proteins (18,500 and 17,000 Mr). The stimulating activity has no effect on the synthesis of proteins from lambda plac5 template. Extracts prepared from cells infected with P4 alpha amber mutants lack this stimulating activity.
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17
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Abstract
A genetic map of satellite bacteriophage P4 has been constructed by means of standard multifactor crosses. The genetic map appears to be a circular permutation of the mature DNA physical map. In addition, a set of markers appear to be linked both to the left and to the right of the same gene alpha. These facts suggest that the P4 genetic map is circular. Since terminal redundancy and/or cyclic permutation are not known to be present in P4 mature DNA, the circularity of P4 genetic map may reflect the physical circularity of the molecules involved in the recombination process. The low frequency of recombination and the strong negative interference observed are in agreement with the above hypothesis.
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18
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Nicoletti M, Bertani G. DNA fusion product of phage P2 with plasmid pBR322: a new phasmid. MOLECULAR & GENERAL GENETICS : MGG 1983; 189:343-7. [PMID: 6343796 DOI: 10.1007/bf00337829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The chromosome of the temperate bacteriophage P2 and that of the plasmid pBR322 have been joined in vitro after treatment with restriction endonuclease EcoRI. The fusion product - a phasmid - can behave as a plasmid, as a phage and as a prophage. It can replicate its DNA under the control of either the specific replication mechanism of the parent phage in a polA mutant or that of the parent plasmid in a rep mutant. Several interesting interactions between the two replication modes are indicated. In particular, phage particles may be produced even when the phage mode of DNA replication is blocked, and this throws new light on the involvement of the early gene A in the regulation of late gene expression in phage P2.
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19
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Funnell BE, Inman RB. Physical evidence for early transcription in intracellular bacteriophage P2 DNA. J Mol Biol 1982; 154:85-101. [PMID: 6281438 DOI: 10.1016/0022-2836(82)90419-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Lindqvist BH. Recombination between satellite phage P4 and its helper P2. II. In vitro construction of a helper-independent P4: :P2 hybrid phage. Gene 1981; 14:243-50. [PMID: 6271625 DOI: 10.1016/0378-1119(81)90157-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [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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Liu LF, Perkocha L, Calendar R, Wang JC. Knotted DNA from bacteriophage capsids. Proc Natl Acad Sci U S A 1981; 78:5498-502. [PMID: 6272306 PMCID: PMC348773 DOI: 10.1073/pnas.78.9.5498] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The majority of the DNA prepared from tailless capsids of bacteriophage P2 by the phenol extraction procedure consists of monomeric rings that have their cohesive ends joined. Electron microscopic and ultracentrifugal studies indicate that these molecules have a complex structure that is topologically knotted; they have a more compact appearance and a higher sedimentation coefficient when compared with regular nicked P2 DNA rings. Linearization of these rings by thermal dissociation or repair of the cohesive ends by DNA polymerase I in the presence of all four deoxynucleoside triphosphates gives molecules that are indistinguishable from normal P2 DNA that has been similarly treated. The knotted nature of the majority of P2 head DNA is further supported by analyzing the products when these molecules are treated with ligase and the ligase-treated molecules are subsequently nicked randomly with DNase I. The data are consistent with the notion that, if such a molecule is first converted to a form that contains only one single-chain scission per molecule, strand separation gives a linear strand and a highly knotted single-stranded ring. The results suggest that the DNA packaged in tailless P2 capsids is arranged in a way that leads to the formation of a complex knot when the ends join. In an intact phage particle, the anchoring of one terminus of the DNA to the head-proximal end of the tail [Chattoraj, D. K. & Inman, R. B. (1974) J. Mol. Biol. 87, 11-22] presumably diminishes or prevents this kind of joining. The novel knotted DNA can be used to assay type II DNA topoisomerases that break and rejoin DNA in a double-stranded fashion.
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22
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Rosner A, Gutstein R, Aviv H. Isolation of viable deletion mutants of Streptomyces actinophage (Pal 6) and their molecular characterization. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:337-41. [PMID: 6248725 DOI: 10.1007/bf00270481] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Deletion mutants of bacteriophage Pal 6 were isolated by successive treatments of either heat (60 degrees C) or pyrophosphate (10 mM). These mutants were characterized by restriction enzyme cleavage analysis. The pyrophosphate resistant clones lost the whole Eco R1 fragment in which the Sal I site is located, as well as an unrelated Hind III fragment. These results show that the region containing the Sal I site in the phage genome is not essential for phage viability. This single Sal I site is therefore suitable as a potential insertion site for DNA cloning. On the other hand, the heat resistant clones that were isolated and characterized do not appear to have detectable deletions as indicated by their Eco R1 DNA digestion pattern.
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23
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Hudnik-Plevnik T, Bertani G. Recombination in bacteriophage P2: recA dependent enhancement by ultraviolet irradiation and by transfection with mixed DNA dimers. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:131-41. [PMID: 6929945 DOI: 10.1007/bf00267221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacteriophage P2 is known for its exceptionally low rate of spontaneous (non-integrative) recombination, which however may be stimulated by ultraviolet irradiation of the phage. We show here that ligated dimers, made in vitro from mixtures of DNAs of two P2 mutants, upon transfection of lysozyme-spheroplasts give origin to recombinants at high frequency. While spontaneous P2 recombination occurs independently of the main recombination pathway of the bacteria, P2 recombinant formation following either ultraviolet irradiation or transfection with DNA dimers requires at least some element of such a pathway, since it is absent or greatly reduced in recA- bacteria or spheroplasts. It would seen that, in the course of its lytic development, P2 deploys a mechanism that inhibits the main recombination pathway of the host cell, or assumes DNA configurations refractory to it.
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Chattoraj DK, Bertani G. Further physical characterization of deletion and substitution mutants affecting the control of lysogeny in bacteriophage P2. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:85-90. [PMID: 6991882 DOI: 10.1007/bf00267216] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A deletion of phage P2, del6 (L.E. Bertani, 1980), thought to remove the structural gene int, and a deletion/substitution, vir94, thought to remove genes int, C and cox, were mapped by electron microscopy, using the heteroduplex technique. Four independent deletion/substitution mutations, all affecting the regulatory region of P2, were compared in all possible combinations with the same technique: two showed sequence homology in their substitution DNA. The results confirm the model proposed for the origin of these mutants, analogous to that for the origin of transducing variants in phage lambda, but suggest in first approximation that the exchange between the P2 DNA and the chromosome of the host bacterium may occur at several different bacterial sites. A map of the regulatory region of P2, based on all data available from the study of deletions and insertions, is presented.
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Westöö A, Ljungquist E. Cloning of the immunity repressor determinant of bacteriophage P2 in the pBR322 plasmid. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:101-9. [PMID: 6247614 DOI: 10.1007/bf00267218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Through in vitro recombination of DNA restriction fragments, we have constructed a plasmid, which expressed in vivo the immunity repressor gene (C) of bacteriophage P2. A bacterial strain carrying such a plasmid showed a high level of P2 specific immunity. It was lysogenized normally by an infecting P2, but the frequency of spontaneous phage production was reduced about 10(4) fold as compared to a normal P2 lysogen. Satellite phage P4, known to derepress P2 lysogens, was unable to derepress the plasmid-carrying lysogenic strain so to allow growth of coinfecting P2. Phage P4 multiplied on the plasmid-carrying, P2-lysogenic strain, but due to a prolonged latent period failed to form plaques on this strain.
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Bertani LE. Genetic interaction between the nip1 mutation and genes affecting integration and excision in phage P2. MOLECULAR & GENERAL GENETICS : MGG 1980; 178:91-9. [PMID: 6991884 DOI: 10.1007/bf00267217] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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27
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Bertani G, Chattoraj DK. Tandem pentuplication of a DNA segment in a derivative of bacteriophage P2: its use in the study of the mechanism of DNA annealing. Nucleic Acids Res 1980; 8:1339-56. [PMID: 7433123 PMCID: PMC323995 DOI: 10.1093/nar/8.6.1339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
From a tandem duplication mutant of phage P2, triplication, quadruplication and pentuplication forms were derived. They were recognized by decreased virion heat stability resulting from the increase in DNA content, and were confirmed by electron microscope heteroduplex mapping. These forms of partially repeated DNA are quite stable in P2 because of the low level of recombination typical of this phage. Under conditions normally employed for full DNA renaturation, these high order repeat chromosomes gave often incomplete renaturation over the repeated segments. Based on current models for DNA renaturation, several predictions were made and tested. The results, although not quantitatively exhaustive, indicated that base pairing proceeding from a nucleation site was sufficiently slow to allow a second nucleation to occur with a fair probability over a length of a few thousand base pairs.
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Westöö A, Ljungquist E. A restriction endonuclease cleavage map of bacteriophage P2. MOLECULAR & GENERAL GENETICS : MGG 1979; 171:91-102. [PMID: 286153 DOI: 10.1007/bf00274019] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A restriction endonuclease cleavage map of phage P2 was constructed. The enzymes used and, within parenthesis, the number of their cleavage sites on the P2 lg cc DNA molecule were: AvaI(3), BalI(1), BAMI(3), BglII(3), HaeIII (more than 40; only three were mapped), HindIII(0), HpaI(10), KpnI(3), PstI(3), SalI(2) and SmaI(2). The EcoRI cleavage sites (3), as determined earlier, were used as reference points for this study. The DNAs of a variety of P2 mutants carrying chromosomal aberrations (dell, del2, del3, del6, vir22, vir37(2), vir79 and vir94) were also similarly examined.
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Ghisotti D, Zangrossi S, Sironi G. X-ray sensitivity of Escherichia coli lysogenic for bacteriophage P2. MOLECULAR & GENERAL GENETICS : MGG 1979; 169:229-35. [PMID: 372744 DOI: 10.1007/bf00382268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Strains of Escherichia coli C or K lysogenic for the non-inducible phage P2 show a lower survival following X-ray irradiation as compared to nonlysogenic strains. This difference in X-ray sensitivity is not accompanied by a significant difference in X-ray induced mutability. The capacity of X-irradiated P2 lysogens to multiply any of a number of unirradiated infecting phages is severely impaired. These effects of X-ray treatment can be most simply explained as a consequence of the fact that protein and RNA syntheses are strongly inhibited in P2 lysogens after X-irradiation. All the above events specifically occurring in X-rayed P2 lysogens are dependent on the P2 gene old.
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30
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Kroyer JM, Dean DH. Isolation and rapid screening of deletion mutants of temperateBacillus subtilis molecular cloning vehicle ρ14. Curr Microbiol 1979. [DOI: 10.1007/bf02603133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Geisselsoder J, Chidambaram M, Goldstein R. Transcriptional control of capsid size in the P2:P4 bacteriophage system. J Mol Biol 1978; 126:447-56. [PMID: 370404 DOI: 10.1016/0022-2836(78)90051-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Flock JI. Deletion mutants of temperate Bacillus subtilis bacteriophage phi105. MOLECULAR & GENERAL GENETICS : MGG 1977; 155:241-7. [PMID: 202858 DOI: 10.1007/bf00272803] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Six deletion mutants of temperate Bacillus subtilis phage phi105 have been isolated on the basis of their increased resistance to chelating agents. The size and position of the deletions was determined by electronmicroscopy of DNA heteroduplexes. All deletions are located in a region about 55-70% from one end of the DNA molecule, in the right half of the known genetic map of the phage. The segment 55-65% does not contain any genes essential for lytic growth or lysogenization. A gene(s) for immunity is located in a segment 65-70% from the left end. By electronmicroscopy by partially denatured phi105 DNA two A-T rich regions have been localized in the right half of the molecule. One of these regions falls within the non-essential 55-65% DNA segment.
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Chatteroraj DK, Oberoi YK, Bertani G. Restriction of bacteriophage P2 by the Escherichia coli RI plasmid, and in vitro cleavage of its DNA by the EcoRI endonuclease. Virology 1977; 81:460-70. [PMID: 331662 DOI: 10.1016/0042-6822(77)90161-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Nilsson E, Bertani LE. Restoration of immunity in lysogens carrying prophage P2, derepressed at high temperature. ACTA ACUST UNITED AC 1977. [DOI: 10.1007/bf00267185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Barrett KJ, Marsh ML, Calendar R. Interactions between a satellite bacteriophage and its helper. J Mol Biol 1976; 106:683-707. [PMID: 789896 DOI: 10.1016/0022-2836(76)90259-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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Sunshine M, Six E. Relief of P2 bacteriophage amber mutant polarity by the satellite bacteriophage P4. J Mol Biol 1976; 106:673-82. [PMID: 789895 DOI: 10.1016/0022-2836(76)90258-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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Pruss GJ, Wang JC, Calendar R. In vitro packaging of covalently closed circular monomers of bacteriophage DNA. J Mol Biol 1975; 98:465-78. [PMID: 1104873 DOI: 10.1016/s0022-2836(75)80080-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Younghusband HB, Egan JB, Inman RB. Characterization of the DNA from bacteriophage P2-186 hybrids and physical mapping of the 186 chromosome. MOLECULAR & GENERAL GENETICS : MGG 1975; 140:101-10. [PMID: 1105151 DOI: 10.1007/bf00329778] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The DNA from two P2-186 hybrid phages and three 186 Insertion mutants have been characterized by heteroduplex analysis and denaturation mapping. The results allow the orientation of the physical and genetic maps of bacteriophage 186 DNA and put physical limits on the chromosomal locations of the phage attachment sites, immunity genes and tail genees.
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40
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Bradley C, Ling OP, Egan JB. Isolation of phage P2-186 intervarietal hybrids and 186 insertion mutants. MOLECULAR & GENERAL GENETICS : MGG 1975; 140:123-35. [PMID: 1105153 DOI: 10.1007/bf00329780] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Intervarietal hybrids formed between coliphages P2 and 186 have been isolated and their preliminary genetic characterization described. Three insertion mutants of 186 have also been isolated.
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41
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Six EW. The helper dependence of satellite bacteriophage P4: which gene functions of bacteriophage P2 are needed by P4? Virology 1975; 67:249-63. [PMID: 1099784 DOI: 10.1016/0042-6822(75)90422-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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42
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Sunshine M, Usher D, Calendar R. Interaction of P2 bacteriophage with the dnaB gene of Escherichia coli. J Virol 1975; 16:284-9. [PMID: 1097733 PMCID: PMC354666 DOI: 10.1128/jvi.16.2.284-289.1975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The dnaB gene product of Escherischia coli is required for multiplication of temperate phage P2. At 37 C in dnaB-ts mutnats, P2 will not plaque and gives a very small burst of progeny. P2 mutants have been isolated which can grow well enough to plaque under these conditions. This type of phage mutant is cis dominant, and one such mutant (P2rlb1) has been mapped near the left end of the early gene B and to the right of the cox4 (excision) mutation. The rlb1 mutation does not lie at the replication origin, but may affect transcription in the early region, which includes the replication origin. It may also represent a site on the P2 DNA which interacts with the dnaB gene product.
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