Changes in the structure and activity of λ DNA in a superinfected immune bacterium

Bode, Vernon C.; Kaiser, A.D.

doi:10.1016/s0022-2836(65)80190-5

Cited by 236 publications

(29 citation statements)

References 27 publications

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“…In neutral buffer containing a high salt concentration (1 M NaCl) or no salt, the sedimentation rate of the slower component was essentially constant, but the faster component sedimented 1.3-times and 1.5-times faster than the slower component in the presence of a high salt concentration and no salt, respectively. This relationship is identical to that of the cc and oc forms of XDNA reported by Bode and Kaiser (11). Moreover, the rates of sedimentation of the faster and slower components were the same as those of the cc and oc forms, respectively of purified Xdvl DNA.…”

Section: Methodssupporting

confidence: 88%

Isolation of Circular DNA Molecules from Whole Cellular DNA by Use of ATP-Dependent Deoxyribonuclease

Mukai

Matsubara

Takagi

1973

Proc. Natl. Acad. Sci. U.S.A.

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Recently, it was shown that ATP-dependent deoxyribonuclease acts upon linear DNA molecules and single-stranded circular molecules, hydrolyzing them into small, acid-soluble fragments. However, the enzyme does not attack doublestranded circular DNA molecules either of the cc or oc form (4-6). Due to this unique property, the enzyme can be used to isolate both cc and oc molecules from a mixture containing a large amount of linear DNA molecules, such as that originating from chromosomes as a result of shear fragmentation.

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Section: Methodssupporting

confidence: 88%

Isolation of Circular DNA Molecules from Whole Cellular DNA by Use of ATP-Dependent Deoxyribonuclease

Mukai

Matsubara

Takagi

1973

Proc. Natl. Acad. Sci. U.S.A.

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“…If cells are infected with a single virus particle, the viral DNA is rapidly converted to a circular form [36][37][38], that being the only cohesion product possible for the newly entered DNA. However, if two or more phage particles inject their DNA into one cell, the concentration of viral DNA within the cell is in the range where concatemers would form in vitroyet the actual product formed upon injection at such multiplicities is the circular monomer.…”

Section: Cyclization Of Lambda Dnamentioning

confidence: 99%

Macromolecular crowding and the mandatory condensation of DNA in bacteria

1996

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Cellular DNA in bacteria is localized into nucleoids enclosed by cytoplasm. The forces which cause condensation of the DNA into nucleoids are poorly understood. We suggest that direct and indirect macromolecular crowding forces from the surrounding cytoplasm are critical factors for nucleoid condensation, and that within a bacterial cell these crowding forces are always present at such high levels that the DNA is maintained in a condensed state. The DNA affected includes not only the preexisting genomic DNA but also DNA that is newly introduced by viral infection, replication or other means.Key words: Cytoplasmic macromolecule; DNA condensation; Escherichia coli; Macromolecular crowding; Mandatory condensation; Nucleoid DNA condensation in bacteria: general considerationsThe genomic DNA of bacteria is condensed into one or a few nucleoids per cell [1] that are in direct contact with a surrounding cytoplasm containing very high concentrations of macromolecules (e.g. ,~ 340 mg/ml of total RNA and protein [2]). The term 'condensation' is used to indicate adoption of a relatively concentrated, compact state occupying a fraction of the volume available. The DNA of the bacterial nucleoid is estimated to have a local concentration of ,'-50-100 mg DNA/ml (see footnote 6 of [3]) and to occupy 1/8 to 1/5 of the volume within the cell envelope [1].Condensation of DNA within bacterial ceils has been observed by light microscopy of both living and fixed cells, as well as by electron microscopy [4][5][6][7][8] (reviewed in [9,10]). Condensation of DNA in isolated nucleoids is indicated by microscopy as well as by hydrodynamic properties [11][12][13]. Condensation of DNA in model in vitro systems has been assayed by aggregation, as described below. Condensing forcesThe origins and magnitudes of the forces which cause DNA condensation are poorly understood. Supercoiling, macromolecular crowding and the binding of histone-like proteins and of polyamines have all been suggested to contribute to DNA condensation. It is unclear how important each of these fac-*Corresponding author: Fax: (1) (301) 496-0201.0014-5793196/$12.00 © 1996 Federation of European Biochemical Societies. PH SO0 1 4-5793(96)00725-9 tors is in causing DNA condensation in vivo. Model studies of the binding of histone-like proteins under dilute solution conditions indicate that the cellular amounts of DNA-binding proteins in bacteria are 5-10-fold lower than those required for condensation (see [14] for references and discussion). The polyamines putrescine and spermidine can occur in large amounts in E. coli [15]. Spermidine but not putrescine can condense DNA from aqueous solution [16], although the binding reaction is relatively salt-sensitive [17,18] and so may make a restricted contribution over much of the range of intracellular salt concentrations observed in growing cells [19,20]. Enzymatic supercoiling directly yields more compact forms [21].Macromolecular crowding ('crowding', reviewed in [22,23]) can cause DNA condensation by two distinctly dif...

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“…Kan R colonies appeared on Kan plates only when the infected bacteria were first allowed to grow in LB for at least 60 min (data not shown). The time required for 90% of particles to adsorb and transfer their DNA through the bacterial membrane is approximately 5 min at 37ЊC (20). Since such rapid transfer can occur even through isolated bacterial membranes (21), it is very likely that only a few minutes were required for DNA to enter the bacteria.…”

Section: Expression Of New Kan R Mutations In Stored Culturesmentioning

confidence: 99%

5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli

Lieb¹,

Rehmat²

1997

Proc. Natl. Acad. Sci. U.S.A.

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Spontaneous deamination of 5-methylcytosine (5meC) causes hot spots of C⅐G 3 T⅐A mutations in Escherichia coli and in human cells. In E. coli, the resulting T⅐G mispairs can be corrected to C⅐G by very short patch (VSP) repair, which requires the product of gene vsr. Mutation hot spots in genes of replicating vsr ؉ bacteria are attributable to low Vsr activity. To determine the rate of deamination of 5meC and the efficiency of VSP repair in nondividing bacteria, we used kanamycin-sensitive (Kan S ) lysogens containing a kan ؊ prophage. Deamination of a 5meC in the kan ؊ gene resulted in mutation to kanamycin resistance (Kan R ). Lysogens containing a single kan ؊ prophage per bacterial genome were grown in synthetic medium with limiting amino acids and stored at 15؇C or 37؇C. In the absence of VSP repair, Kan R mutants accumulated at the rate of approximately 1.3 ؋ 10 ؊7 per bacterium per day at 37؇C. This is similar to the 5meC 3 T mutation rate reported for DNA in solution. In vsr ؉ bacteria, the Kan R accumulation rate was 3 ؋ 10 ؊9 per bacterium per day, which is not significantly higher than the rate observed when the target cytosine was unmethylated. The increase in Kan R mutants was barely detectable in vsr ؉ cultures stored at 15؇C for 4 months. It is likely that mutation hot spots at 5meC in rapidly dividing cells are attributable to insufficient time for T⅐G correction in the interval between deamination of 5meC and subsequent DNA replication. DNA synthesis occurred in bacteria starved for amino acids and this synthesis was not highly mutagenic.

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Changes in the structure and activity of λ DNA in a superinfected immune bacterium

Cited by 236 publications

References 27 publications

Isolation of Circular DNA Molecules from Whole Cellular DNA by Use of ATP-Dependent Deoxyribonuclease

Isolation of Circular DNA Molecules from Whole Cellular DNA by Use of ATP-Dependent Deoxyribonuclease

Macromolecular crowding and the mandatory condensation of DNA in bacteria

5-Methylcytosine is not a mutation hot spot in nondividing Escherichia coli

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