51
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Lange CS, Liberman DF, Clark RW, Ferguson P. The organization and repair of DNA in the mammaliam chromosome. I. Calibration procedures and errors in the determination of the molecular weight of native DNA. Biopolymers 1977; 16:1063-81. [PMID: 861365 DOI: 10.1002/bip.1977.360160509] [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: 12/24/2022]
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52
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Manoil C, Sinha N, Alberts B. Intracellular DNA-protein complexes from bacteriophage T4-infected cells isolated by a rapid two-step procedure. Characterization and identification of the protein components. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40520-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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53
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Clark RW, Lange CS. The sucrose gradient and native DNA S20,W, an examination of measurement problems. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 454:567-77. [PMID: 793631 DOI: 10.1016/0005-2787(76)90282-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sedimentation coefficients of T7, T2H AND T4 DNA were determined with isokinetic sucrose gradients in both 0.1 M and 1 M NaCl. The s values were completely equivalent to those measured by analytical ultracentrifuge and no reduction of s20,w was observed due to the presence of sucrose (anomalous sedimentation). s20,w values are calculated on the basis of both partial specific volume (v) and apparent specific volume (0). Using the latter value s20,w molecular weight relations are derived for 0.1 M and 1 M NaCl solvents. The glucosylation of T2H and T4 DNA appears to influence s20,w in a manner disproportionate to the molecular weight added by glucose.
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54
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55
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Hamilton S, Pettijohn DE. Properties of condensed bacteriophage T4 DNA isolated from Escherichia coli infected with bacteriophage T4. J Virol 1976; 19:1012-27. [PMID: 787557 PMCID: PMC354942 DOI: 10.1128/jvi.19.3.1012-1027.1976] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Methods developed for isolating bacterial nucleoids were applied to bacteria infected with phage T4. The replicating pool of T4 DNA was isolated as a particle composed of condensed T4 DNA and certain RNA and protein components of the cell. The particles have a narrow sedimentation profile (weight-average s=2,500S) and have, on average, a T4 DNA content similar to that of the infected cell. Their dimensions observed via electron and fluorescence microscopy are similar to the dimensions of the intracellular DNA pool. The DNA packaging density is less than that of the isolated bacterial nucleoid but appears to be roughly similar to its state in vivo. Host-cell proteins and T4-specific proteins bound to the DNA were characterized by electrophoresis on polyacrylamide gels. The major host proteins are the RNA polymerase subunits and two envelope proteins (molecular weights, 36,000 and 31,000). Other major proteins of the host cell were absent or barely detectable. Single-strand breaks can be introduced into the DNA with gamma radiation or DNase without affecting its sedimentation rate. This and other studies of the effects of intercalated ethidium molecules have suggested that the average superhelical density of the condensed DNA is small. However, these studies also indicated that there may be a few domains in the DNA that become positively supercoiled in the presence of high concentrations of ethidium bromide. In contrast to the Escherichia coli nucleoid, the T4 DNA structure remains condensed after the RNA and protein components have been removed (although there may be slight relaxation in the state of condensation under these conditions).
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56
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Snyder L, Gold L, Kutter E. A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. Proc Natl Acad Sci U S A 1976; 73:3098-102. [PMID: 1067605 PMCID: PMC430943 DOI: 10.1073/pnas.73.9.3098] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
T-even coliphages have 5-hydroxymethylcytosine in their DNA instead of cytosine. In some T4 mutants, the replicated DNA contains cytosine, but then no late gene products are made. We show that the inability to make late gene products with cytosine-containing T4 DNA is due to a T4 gene products. This gene product, while probably nonessential under normal conditions, interacts with an essential part of the transcription apparatus. Mutations in this gene allow viable T4 particles to be made whose DNA has been substituted almost 100% with cytosine.
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57
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58
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Mosig G, Bock S. Gene 32 protein of bacteriophage T4 moderates the activities of the T4 gene 46/47-controlled nuclease and of the Escherichia coli RecBC nuclease in vivo. J Virol 1976; 17:756-61. [PMID: 1255856 PMCID: PMC515474 DOI: 10.1128/jvi.17.3.756-761.1976] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genes 46 and 47 of phage T4 control a nuclease that is required for genetic recombination and may act similarly to the Escherichia coli RecBC nuclease. In vivo, the nucleolytic activities of both of these nucleases must be moderated so that recombining DNA intermediates are not destroyed. We conclude from our present experiments that the phage T4 gene 32 protein, specifically its C-terminal domain, participates in such moderation. We have investigated DNA degradation in different gene 32 and gene 32/46 mutants under conditions that are completely restrictive for progeny production in all the mutants. Under these conditions, DNA of those gene 32 mutants in which the C-terminal domain of the protein is not synthesized or is modified is degraded to acid-soluble material. T4 gene 46 or E. coli recB mutations reduce such degradation; together they abolish it completely. By contrast, single gene 32 mutants which produce an unaltered C-terminal domain show little or no degradation of their DNA. Residual protection against nucleases is unrelated to residual primary DNA replication or to overproduction of the mutant peptides in the different gene 32 mutants.
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59
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Snustad DP, Tigges MA, Parson KA, Bursch CJ, Caron FM, Koerner JF, Tutas DJ. Identification and preliminary characterization of a mutant defective in the bacteriophage T4-induced unfolding of the Escherichia coli nucleoid. J Virol 1976; 17:622-41. [PMID: 768519 PMCID: PMC515453 DOI: 10.1128/jvi.17.2.622-641.1976] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The nucleoids of Escherichia coli S/6/5 cells are rapidly unfolded at about 3 min after infection with wild-type T4 bacteriophage or with nuclear disruption deficient, host DNA degradation-deficient multiple mutants of phage T4. Unfolding does not occur after infection with T4 phage ghosts. Experiments using chloramphenicol to inhibit protein synthesis indicate that the T4-induced unfolding of the E. coli chromosomes is dependent on the presence of one or more protein synthesized between 2 and 3 min after infection. A mutant of phage T4 has been isolated which fails to induce this early unfolding of the host nucleoids. This mutant has been termed "unfoldase deficient" (unf-) despite the fact that the function of the gene product defective in this strain is not yet known. Mapping experiments indicate that the unf- mutation is located near gene 63 between genes 31 and 63. The folded genomes of E. coli S/6/5 cells remain essentially intact (2,000-3,000S) at 5 min after infection with unfoldase-, nuclear disruption-, and host DNA degradation-deficient T4 phage. Nuclear disruption occurs normally after infection with unfoldase- and host DNA degradation-deficient but nuclear disruption-proficient (ndd+), T4 phage. The host chromosomes remain partially folded (1,200-1,800S) at 5 min after infection with the unfoldase single mutant unf39 x 5 or an unfoldase- and host DNA degradation-deficient, but nuclear disruption-proficient, T4 strain. The presence of the unfoldase mutation causes a slight delay in host DNA degradation in the presence of nuclear disruption but has no effect on the rate of host DNA degradation in the absence of nuclear disruption. Its presence in nuclear disruption- and host DNA degradation-deficient multiple mutants does not alter the shutoff to host DNA or protein synthesis.
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60
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Resnick MA, Martin P. The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control. MOLECULAR & GENERAL GENETICS : MGG 1976; 143:119-29. [PMID: 765749 DOI: 10.1007/bf00266917] [Citation(s) in RCA: 429] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
With the use of neutral sucrose sedimentation techniques, the size of unirradiated nuclear DNA and the repair of double-strand breaks induced in it by ionizing radiation have been determined in both wild-type and homozygous rad52 diploids of the yeast Saccharomyces cerevisiae. The number average molecular weight of unirradiated DNA in these experiments is 3.0 X 10(8)+/-0.3 Daltons. Double-strand breaks are induced with a frequency of 0.58 X 10(-10) per Daltonkrad in the range of 25 to 100 krad. Since repair at low doses is observed in wild-type but not homozygous rad52 strains, the corresponding rad52 gene product is concluded to have a role in the repair process. Cycloheximide was also observed to inhibit repair to a limited extent indicating a requirement for protein synthesis. Based on the sensitivity of various mutants and the induction frequency of double-strand breaks, it is concluded that there are 1 to 2 double-strand breaks per lethal event in diploid cells incapable of repairing these breaks.
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61
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Kutter E, Beug A, Sluss R, Jensen L, Bradley D. The production of undegraded cytosine-containing DNA by bacteriophage T4 in the absence of dCTPase and endonucleases II and IV, and its effects on T4-directed protein synthesis. J Mol Biol 1975; 99:591-607. [PMID: 175166 DOI: 10.1016/s0022-2836(75)80174-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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62
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Template properties of bacteriophage T4 vegetative DNA. II. Effect of maturation and DNA-arrest mutations. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)40680-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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63
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Dewey MJ, Frankel FR. Two suppressor loci for gene 49 mutations of bacteriophage T4. II. DNA and capsid maturation. Virology 1975; 68:402-17. [PMID: 1198926 DOI: 10.1016/0042-6822(75)90282-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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64
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Prakash L. Repair of pyrimidine dimers in nuclear and mitochondrial DNA of yeast irradiated with low doses of ultraviolet light. J Mol Biol 1975; 98:781-95. [PMID: 1104879 DOI: 10.1016/s0022-2836(75)80010-6] [Citation(s) in RCA: 133] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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65
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Wu R, Geiduschek EP. The role of replication proteins in the regulation of bacteriophage T4 transcription. I. Gene 45 and hydroxymethyl-C-containing DNA. J Mol Biol 1975; 96:513-38. [PMID: 1104860 DOI: 10.1016/0022-2836(75)90137-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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66
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Coppo A, Manzi A, Pulitzer JF, Takahashi H. Host mutant (tabD)-induced inhibition of bacteriophage T4 late transcription. I. Isolation and phenotypic characterization of the mutants. J Mol Biol 1975; 96:579-600. [PMID: 1195367 DOI: 10.1016/0022-2836(75)90140-0] [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: 12/26/2022]
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67
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Ehrlich M, Ehrlich K, Mayo JA. Unusual properties of the DNA from Xanthomonas phage XP-12 in which 5-methylcytosine completely replaces cytosine. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 395:109-19. [PMID: 1138935 DOI: 10.1016/0005-2787(75)90149-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Xanthomonas phage XP-12 contains 5-methylcytosine completely replacing cytosine. This substitution confers several unusual properties upon XP-12 DNA. The buoyant density of XP-12 DNA in CsCl gradients is 1.710 g/cm-3, 0.16 g/cm-3 lower than that expected for a normal DNA with the same percentage of adenine plus thymine. The melting temperature for XP-12 DNA in 0.012 M Na+ is the highest reported for any naturally occurring DNA, 83.2 degrees C, 6.1 degrees C higher than that of normal DNAs with the same percentage of adenine plus thymine. Unlike the minor amounts of 5-methylcytosine found in most plant and animal DNAs, the 5-methylcytosine residues of XP-12 derive their methyl group from the 3-carbon of serine instead of from the thiomethyl carbon of methionine. .
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68
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Takacs BJ, Rosenbusch JP. Modification of Escherichia coli membranes in the prereplicative phase of phage T4 infection. Specificity of association and quantitation of bound phage proteins. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41722-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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69
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Hamlett NV, Berger H. Mutations altering genetic recombination and repair of DNA in bacteriophage T4. Virology 1975; 63:539-67. [PMID: 163533 DOI: 10.1016/0042-6822(75)90326-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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70
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71
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Parson KA, Snustad DP. Host DNA degradation after infection of Escherichia coli with bacteriophage T4: dependence of the alternate pathway of degradation which occurs in the absence of both T4 endonuclease II and nuclear disruption on T4 endonuclease IV. J Virol 1975; 15:221-4. [PMID: 1089802 PMCID: PMC354438 DOI: 10.1128/jvi.15.1.221-224.1975] [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: 12/25/2022] Open
Abstract
Escherichia coli cells infected with T4 phage which are deficient in both nuclear disruption and endonuclease II exhibit a pathway of host DNA degradation which does not occur in cells infected with phage deficient only in endonuclease II. This alternate pathway of host DNA degradation requires T4 endonuclease IV.
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72
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Tomich PK, Chiu CS, Wovcha MG, Greenberg GR. Evidence for a Complex Regulating the in Vivo Activities of Early Enzymes Induced by Bacteriophage T4. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)81282-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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73
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Snustad DP, Parson KA, Warner HR, Tutas DJ, Wehner JM, Koerner JF. Mutants of bacteriophage T4 deficient in the ability to induce nuclear disruption. II. Physiological state of the host nucleoid in infected cells. J Mol Biol 1974; 89:675-87. [PMID: 4615166 DOI: 10.1016/0022-2836(74)90044-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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74
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Abstract
The role of T7-induced exonuclease (gene 6) in molecular recombination was studied by examining the fate of parental DNA during parental-to-progeny recombination. The method used was to compare infections with T7(+), T7am-6-233 (am gene 6), or T7ts6-136 (ts gene 6) under permissive and nonpermissive conditions. CsCl density gradient analysis of replicative DNA indicated that T7 exonuclease is necessary for recombination to occur, i.e., in the absence of the exonuclease the parental DNA replicated continuously as a hybrid molecule and did not recombine. Further studies under conditions where replicative DNA was denatured and analyzed by CsCl density gradient centrifugation indicated that the exonuclease is also needed for a limited amount of covalent repair of recombinants. A repair function for the T7-induced exonuclease is also suggested by results obtained from alkaline sucrose gradient analysis of replicative DNA. Under conditions nonpermissive for the exonuclease, discontinuities in the DNA accumulated during infection by T7am6-233 or by T7ts6-136.
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75
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76
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Vetter D, Sadowski PD. Point mutants in the D2a region of bacteriophage T4 fail to induce T4 endonuclease IV. J Virol 1974; 14:207-13. [PMID: 4847325 PMCID: PMC355505 DOI: 10.1128/jvi.14.2.207-213.1974] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We have studied the properties of presumptive point mutants in the D2a region of bacteriophage T4. Dominance tests showed that the D2a mutation was recessive to the wild-type allele. The mutations were shown to map in the D2a region by complementation against rII deletions. The D2a mutations were also located between gene 52 and rIIB by two- and three-factor crosses. The mutants are located at at least two distinct loci in the D2a region. The point mutants grow normally on all hosts tested and none of the mutants makes T4 endonuclease IV. We propose the name "denB" for the D2a locus.
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77
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78
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79
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Lange CS, Liberman DF. A semiautomated system for the production and analysis of sucrose density gradients. Anal Biochem 1974; 59:129-45. [PMID: 4601413 DOI: 10.1016/0003-2697(74)90017-7] [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: 01/11/2023]
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80
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Tutas DJ, Wehner JM, Koerner JF. Unfolding of the host genome after infection of Escherichia coli with bacteriophage T4. J Virol 1974; 13:548-50. [PMID: 4589860 PMCID: PMC355330 DOI: 10.1128/jvi.13.2.548-550.1974] [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: 01/11/2023] Open
Abstract
The folded genome of Escherichia coli is converted to a slower-sedimenting form within 5 min after infection with bacteriophage T4 or T4nd28(den A)-amN82(44). Chloramphenicol sensitivity and response to UV-irradiation of the phage suggest participation of viral-induced functions.
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81
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Elliott J, Richter C, Souther A, Bruner R. Synthesis of bacteriophage and host DNA in toluene-treated cells prepared from T4-infected Escherichia coli: role of bacteriophage gene D2a. J Virol 1973; 12:1253-8. [PMID: 4586772 PMCID: PMC356765 DOI: 10.1128/jvi.12.6.1253-1258.1973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We investigated the synthesis of DNA in toluene-treated cells prepared from Escherichia coli infected with bacteriophage T4. If the phage carry certain rII deletion mutations, those which extend into the nearby D2a region, the following results are obtained: (i) phage DNA synthesis occurs unless the phage carries certain DNA-negative mutations; and (ii) host DNA synthesis occurs even though the phage infection has already resulted in the cessation of host DNA synthesis in vivo. The latter result indicates that the phage-induced cessation of host DNA synthesis is not due to an irreversible inactivation of an essential component of the replication apparatus. If the phage are D2a(+), host DNA synthesis in toluene-treated infected cells is markedly reduced; phage DNA synthesis is probably also reduced somewhat. These D2a effects, considered along with our earlier work, suggest that a D2a-controlled nuclease, specific for cytosine-containing DNA, is active in toluene-treated cells.
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82
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83
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Swift RL, Wiberg JS. Bacteriophage T4 inhibits colicin E2-induced degradation of Escherichia coli DNA. 3. Zone sedimentation analyses of the DNA degradation products. J Mol Biol 1973; 80:743-58. [PMID: 4589649 DOI: 10.1016/0022-2836(73)90207-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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84
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Goscin LA, Hall DH. Hydroxyurea-sensitive mutants of T4. II. Degradation and utilization of bacterial DNA. Virology 1973; 56:207-17. [PMID: 4583303 DOI: 10.1016/0042-6822(73)90300-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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85
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Farrell L, Reiter H. Phleomycin-stimulated degradation of deoxyribonucleic acid in Escherichia coli. Antimicrob Agents Chemother 1973; 4:320-6. [PMID: 4586146 PMCID: PMC444550 DOI: 10.1128/aac.4.3.320] [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: 01/11/2023] Open
Abstract
Phleomycin stimulates the degradation of DNA by energy-dependent endonuclease and exonuclease reactions in Escherichia coli rec(+) cells and in recB(-) and recC(-) cells that lack an adenosine triphosphate-dependent nuclease functioning in the repair of ultraviolet (UV) lesions. Exonuclease activity is blocked in T4 phage-infected cells. The endonuclease reaction produces 10(7)-dalton segments resembling those produced in colicin E2-treated cells. These differ from the random-sized segments produced in UV-irradiated cells, or the 10(6)-dalton segments made in T4 phage-infected cells. A mutant selected for phleomycin tolerance is cross-tolerant to colicin E2, and some mutants selected for colicin E2 tolerance are cross-tolerant to phleomycin. On the basis of these cross-tolerances and the similarities between the effects of phleomycin and E2-stimulated nucleases, the suggestion is made that both agents may stimulate the same nuclease reactions in E. coli cells.
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86
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Shah DB, Berger H. Effect of a gene-specific suppressor mutation (das) on DNA synthesis of gene 46-47 mutants of bacteriophage T4D. J Virol 1973; 12:328-33. [PMID: 4583888 PMCID: PMC356627 DOI: 10.1128/jvi.12.2.328-333.1973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mutants in genes 46 and 47 of bacteriophage T4 exhibit early cessation of DNA synthesis, inability to form a normal rapidly sedimenting DNA intermediate (200S), reduced genetic recombination, and reduced viable phage production. A gene-specific suppressor mutation called das partially restores many of the pleiotropic effects of gene 46-47 mutants (13). Our results indicate that this partial suppression by das is associated with (i) the synthesis of a small fraction of DNA containing long single chains not detectable in 46-47 infection and (ii) a decrease in an "early" function which participates in the degradation of DNA synthesized in the absence of 46-47 functions. However, das does not restore the formation of a normal rapidly sedimenting (200S) DNA intermediate.
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87
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Wovcha MG, Tomich PK, Chiu CS, Greenberg GR. Direct participation of dCMP hydroxymethylase in synthesis of bacteriophage T4 DNA. Proc Natl Acad Sci U S A 1973; 70:2196-200. [PMID: 4525160 PMCID: PMC433700 DOI: 10.1073/pnas.70.8.2196] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In order to retain in an in situ system the control mechanisms involved in synthesis of bacteriophage T4 DNA, infected cells were made permeable to nucleotides by plasmolysis with concentrated sucrose. Such preparations use exogenous deoxyribonucleotides to synthesize T4 phage DNA. As has been observed with in vivo studies, DNA synthesis was drastically reduced in plasmolyzed preparations from cells infected by amber mutants of genes 1, 32, 41, 42, 43, 44, or 45. Added 5-hydroxymethyl dCTP did not bypass either a mutant of gene 42 (dCMP hydroxymethylase) or of gene 1 (phage-induced deoxyribonucleotide kinase). In a phage system lacking deoxycytidine triphosphatase (gene 56) and the gene-46 product, and therefore incorporating dCTP into DNA, dCTP incorporation did not require dCMP hydroxymethylase, in keeping with in vivo results. With a triple amber mutant of genes 1, 46, and 56 only slight incorporation of dCTP occurred. By contrast, in experiments performed in vivo the synthesis of cytosine-containing DNA was unaffected by an amber mutation in gene 1. These studies provide evidence that dCMP hydroxymethylase, in addition to its known catalytic function, has a second, more direct, role in phage T4 DNA synthesis, apparently in recognition of hydroxymethyl dCTP. The role of the phage-induced deoxyribonucleotide kinase in T4 DNA synthesis in the plasmolyzed system remains unresolved.
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88
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Almendinger R, Hager LP. Reconstitution of colicin E2-induced deoxyribonucleic acid degradation in spheroplast preparations. Antimicrob Agents Chemother 1973; 4:167-77. [PMID: 4598217 PMCID: PMC444523 DOI: 10.1128/aac.4.2.167] [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: 01/11/2023] Open
Abstract
Spheroplasts are insensitive to colicin E(2) and do not show deoxyribonucleic acid (DNA) degradation even in the presence of massive amounts of E(2). However, when both endonuclease I and E(2) were present, spheroplast DNA was degraded by an endonucleolytic activity which gave rise primarily to double-strand DNA cleavages, producing fragments having an average molecular weight of 9 x 10(6). Pancreatic ribonuclease could substitute for colicin E(2) in the reconstitution system, but pancreatic deoxyribonuclease could not replace endonuclease I. However, colicin E(2) could not activate transfer ribonucleic acid-inhibited endonuclease I in an in vitro system where pancreatic ribonuclease caused full stimulation.
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89
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McNicol LA, Goldberg EB. An immunochemical characterization of glucosylation in bacteriophage T4. J Mol Biol 1973; 76:285-301. [PMID: 4579548 DOI: 10.1016/0022-2836(73)90392-6] [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: 01/11/2023]
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90
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91
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Earhart CF, Sauri CJ, Fletcher G, Wulff JL. Effect of inhibition of macromolecule synthesis on the association of bacteriophage T4 DNA with membrane. J Virol 1973; 11:527-34. [PMID: 4573364 PMCID: PMC355134 DOI: 10.1128/jvi.11.4.527-534.1973] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The "Mg(2+)-Sarkosyl crystals" (M band) technique distinguishes between membrane-bound and free intracellular DNA. This procedure was employed to investigate the nature of the reactions necessary to convert input T4 DNA to a rapidly sedimenting form. Energy poisoning inhibits this attachment reaction. Neither protein nor DNA synthesis appears to be required, but experiments with rifampin and extensively irradiated T4 suggest that RNA synthesis is involved. These results were confirmed by a second procedure for the determination of rapidly sedimenting DNA.
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92
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Swift RL, Wiberg JS. Bacteriophage T4 inhibits colicin E2-induced degradation of Escherichia coli deoxyribonucleic acid. II. Inhibition by T4 ghosts and by T4 in the absence of protein synthesis. J Virol 1973; 11:386-98. [PMID: 4570926 PMCID: PMC355114 DOI: 10.1128/jvi.11.3.386-398.1973] [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: 01/11/2023] Open
Abstract
The deoxyribonucleic acid (DNA) of Escherichia coli B is converted by colicin E2 to products soluble in cold trichloroacetic acid; we showed previously that this DNA degradation (hereafter termed solubilization) is subject to inhibition by infection with phage T4 and that at least two modes of inhibition can be differentiated on the basis of their sensitivity to chloramphenicol (CM). This report deals exclusively with the inhibition of E2 produced by T4, or T4 ghosts, in the absence of protein synthesis. The following observations are described. (i) The stage of T4 infection that inhibits E2 occurs after reversible adsorption of the phage to the bacterial surface, but probably prior to injection of T4 DNA into the cell's interior. (ii) The extent of inhibition increases as the T4 multiplicity is increased; however, the fraction of bacterial DNA that eventually is solubilized is virtually independent of the phage multiplicity. (iii) Phage ghosts (DNA-less phage particles) possess an approximately 15-fold greater inhibitory capacity toward E2 than do intact phage; however, because highly purified T4 (completely freed of ghost contamination) still inhibit E2, we discount the possibility that preparations of "intact phage" inhibit exclusively by virtue of contaminating ghosts. (iv) T4 infection does not liberate an extracellular inactivator of E2. In fact, infection with sufficiently high multiplicities of T4 produces a supernatant factor that protects E2 from nonspecific inactivation at 37 C. This protective factor does not interfere with the colicin's ability to induce DNA solubilization. (v) Inhibition of E2 occurs even when phage are added well after initiation of DNA solubilization by E2, suggesting that a late stage of E2 action is the target of inhibition by T4 infection. (vi) Increasing the CM concentration from 50 mug/ml to 200 mug/ml appears to reduce the inhibition appreciably; however, this can be attributed to an enhancement by CM of the rate of E2-induced DNA solubilization. (vii) The same degree of inhibition of E2 by T4 seen in CM is observed when CM is replaced by puromycin or rifampin. (viii) Others have shown that raising the multiplicity of E2 increases the rate of DNA solubilization. We find that the fractional inhibition (i), [i = (1 - y(i)/y(o)), where y(i) and y(o) represent the inhibited and uninhibited rates of solubilization of DNA, respectively], produced by a given T4 multiplicity is independent of the multiplicity of E2 and hence is independent of the rate of DNA solubilization induced by E2.
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93
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Scholz D, Mann W, Hansen S, Korb C, Rosenthal HA. [Studies of bacteriophage T3. V. Further characterization of 2 temperature-sensitive mutants, ts21 and ts25, in Escherichia coli B and E. coli AB 2500]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1973; 13:657-71. [PMID: 4592537 DOI: 10.1002/jobm.3630130804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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94
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Smith DW. DNA synthesis in prokaryotes: replication. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973; 26:321-408. [PMID: 4122629 DOI: 10.1016/0079-6107(73)90022-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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95
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Prashad N, Hosoda J. Role of genes 46 and 47 in bacteriophage T4 reproduction. II. Formation of gaps on parental DNA of polynucleotide ligase defective mutants. J Mol Biol 1972; 70:617-35. [PMID: 4563264 DOI: 10.1016/0022-2836(72)90562-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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96
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Matin A, Rittenberg SC. Kinetics of deoxyribonucleic acid destruction and synthesis during growth of Bdellovibrio bacteriovorus strain 109D on pseudomonas putida and escherichia coli. J Bacteriol 1972; 111:664-73. [PMID: 4559819 PMCID: PMC251338 DOI: 10.1128/jb.111.3.664-673.1972] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
During the growth of Bdellovibrio bacteriovorus on Pseudomonas putida or Escherichia coli in either 10(-3)m tris(hydroxymethyl)aminomethane or in dilute nutrient broth, the host deoxyribonucleic acid (DNA) was rapidly degraded, and by 30 to 60 min after the initiation of the bdellovibrio development cycle essentially all host DNA became nonbandable in CsCl gradients. At this stage the host DNA degradation products were nondiffusable, and there was no appreciable pool of low-molecular-weight (cold acid soluble) DNA fragments in the cells or in the suspending medium. Bdellovibrio DNA synthesis occurred only after degradation of host DNA to a nonbandable form was complete. The synthesis occurred in a continuous fashion with P. putida as the host and in two separate periods with E. coli as host. By using E. coli containing a (3)H-thymidine label, it was shown that 73%, on the average, of the thymine residues of host DNA were incorporated into bdellovibrio DNA when E. coli was the only source of nutrient. In the presence of dilute nutrient broth, the host cells still served as the major source of precursors for bdellovibrio DNA synthesis, with only 20% of the precursors arising from the exogenous nutrients. The data indicate an efficient and controlled utilization of host DNA by the bdellovibrio. The host DNA is apparently degraded early in the developmental cycle to oligonucleotides of intermediate molecular weight from which the biosynthetic monomers are generated only as they become needed for bdellovibrio DNA synthesis.
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97
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Hattman S. Methylation of adenine residues in bacteriophage T2 DNA containing cytosine in place of 5-hydroxymethylcytosine. Virology 1972; 49:404-12. [PMID: 4340808 DOI: 10.1016/0042-6822(72)90493-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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98
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Bruner R, Souther A, Suggs S. Stability of cytosine-containing deoxyribonucleic acid after infection by certain T4 rII-D deletion mutants. J Virol 1972; 10:88-92. [PMID: 4339199 PMCID: PMC356429 DOI: 10.1128/jvi.10.1.88-92.1972] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
When T-even phage infect Escherichia coli, synthesis of host deoxyribonucleic acid (DNA) rapidly ceases. If the phage carry a mutation in a gene essential for phage DNA synthesis, then the infected bacteria should make no DNA, either host DNA or phage DNA. However, we have found that infection with certain T4 gene 56 (deoxycytidine triphosphatase)-rII double mutants leads to substantial DNA synthesis. Only rII deletion mutations which extend into the middle third of the adjacent, nonessential D region lead to the anomalous DNA synthesis, when combined with a gene 56 mutation; the requirement probably is that the deletion extend into the D2a transcriptional unit identified by Sederoff et al. Genetic evidence indicates that the observed anomalous DNA synthesis is synthesis of phage DNA. We suggest that the D2a region controls, directly or indirectly, a nuclease involved in the breakdown of cytosine-containing DNA. In the absence of the D2a product, the cytosine-containing phage DNA made by the gene 56 mutant is stabilized.
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99
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Cascino A, Riva S, Geiduschek EP. Host DNA synthesis after infection of Escherichia coli with mutants of bacteriophage T4. Virology 1971; 46:437-52. [PMID: 4943194 DOI: 10.1016/0042-6822(71)90044-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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100
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Specific suppression of mutations in genes 46 and 47 by das, a new class of mutations in bacteriophage T4D. J Virol 1971; 8:603-12. [PMID: 4943681 PMCID: PMC376237 DOI: 10.1128/jvi.8.5.603-612.1971] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mutants in T4 genes 46 and 47 exhibit early cessation of deoxyribonucleic acid (DNA) synthesis ("DNA arrest") and decreased synthesis of late proteins and phage. In addition, mutants in genes 46 and 47 fail to degrade host DNA to acidsoluble products. It is shown here that this complex phenotype can be partially suppressed by mutation of a T4 gene external to genes 46 and 47 which has been named das for "DNA arrest suppressor." The das mutations were discovered as third-site mutations in spontaneous pseudorevertants of [46, 47] mutants; the pseudorevertants make small plaques on Escherichia coli B, whereas [46, 47] mutants make none. The [das, 46, 47] triple mutant exhibits increased DNA, late protein, and viable phage production compared to the double mutant [46, 47]. The [das, 46, 47] mutant also degrades more of the host DNA to acid-soluble products than does the [46, 47] mutant. The suppressor effect of the das mutation appears to be gene-specific: it suppresses both amber and temperature-sensitive mutations in genes 46 and 47 and does not suppress amber mutations in any of the other genes tested. The [das] single mutants make normal-sized plaques on E. coli B and exhibit nearly normal host DNA degradation, DNA synthesis, late protein synthesis, and viable phage production. The das mutations either define a new gene between genes 33 and 34 or are special mutations within gene 33.
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