Evidence that adenine methylation influences DNA-protein interactions in Escherichia coli

Biological role of DNA methylation: sequence-specific single-strand breaks associated with hypomethylation of GATC sites in Escherichia coli DNA

The effect of methylation of GATC sites in Escherichia coli DNA on the formation of single-strand breaks was studied with dam+, dam mutant, and Dam-overproducer strains. Single-strand breaks have been observed in dam mutant cells predominantly at TpT and, to a lesser extent, at CpC. In dam mutant cells harboring pTP166 (a plasmid containing the dam gene), no such nicks were observed.

Regulation of transcription of the chromosomal dnaA gene of Escherichia coli

By comparative S1 analysis we investigated the in vivo regulation of transcription of the chromosomal dnaA gene coding for a protein essential for the initiation of replication at the chromosomal origin. Inactivation of the protein in dnaA mutants results in derepression, whereas excess DnaA protein (presence of a DnaA overproducing plasmid) leads to repression of dnaA transcription. Both dnaA promoters are subject to autoregulation allowing modulation of transcriptional efficiency by at least 20-fold. Increasing the number of oriC sequences (number of DnaA binding sites) in the cell by introducing oriC plasmids leads to a derepression of transcription. Autoregulation and binding to oriC suggest that the DnaA protein exerts a major role in the regulation of the frequency of initiation at oriC. The efficiency of transcription of the dnaA2 promoter is reduced in the absence of dam methylation, which is involved in the regulation of oriC replication.

Novel regulatory mutants of the phosphate regulon in Escherichia coli K-12

New pleiotropic mutants were isolated that express either the phoA, psiE or psiO promoter constitutively and simultaneously alter bacterial alkaline phosphatase regulation, carbon utilization or ultraviolet light sensitivity. To do this, Lac+ mutants were isolated from strains with the appropriate lacZ transcriptional fusions. Over 300 independent mutants were characterized, and all that constitutively express phoA map in phoR, phoU, the phosphate-specific transport system or a new locus called phoF. However, only phoU mutants express both phoA and psiE constitutively. Carbohydrate-utilizing mutants that show constitutive expression of psiE and psiO map in cya, crp and, possibly, crr. Also, numerous ultraviolet-light-sensitive mutants were discovered that show increased psiO expression and map in lon. Some other mutations that lead to constitutive psiO expression (which is normally induced either by phosphate, nitrogen or carbon starvation or anoxia) show decreased expression of phoA. Also, several mutants were found that show an unusual metastable character affecting psiO or phoA transcription. In these, colonies spontaneously switch between an induced and repressed "state" with respect to lac or bacterial alkaline phosphatase expression. In some, the clonal variation of the lactose phenotype or bacterial alkaline phosphatase synthesis is recA-independent and phenotypically resembles phase variation in Salmonella typhimurium. The latter class are called "phase mutants". The mutants are discussed in terms of protein-nucleic acid interactions and/or possible changes in the DNA, i.e. modifications or rearrangements, within the phosphate gene system, that are physiologically regulated.

Mutant of Salmonella typhimurium LT2 deficient in DNA adenine methylation

A mutant of Salmonella typhimurium LT2 deficient in methylation of the adenine residues in the sequence 5'-GATC-3' was isolated. The mutation (dam-1) was linked to the cysG locus, and the properties of the mutant were similar to those of Escherichia coli dam mutants. Reversion of the hisC3076 frameshift marker by 9-aminoacridine was substantially enhanced by the dam-1 mutation, implying a direct role for adenine methylation in the prevention of frameshift mutation induction.

A human DNA-binding protein is methylation-specific and sequence-specific

A nuclear protein isolated from human placenta, methylated DNA-binding protein (MDBP), binds selectively to DNA enriched in 5-methylcytosine. We now demonstrate that MDBP is a sequence-specific, as well as methylation-specific, DNA-binding protein. From ten restriction fragments of pBR322 DNA methylated with human DNA methyltransferase, one was bound to MDBP very much more strongly than any of the others. For this preferential binding to MDBP, the DNA had to be methylated. By a DNase I protection experiment (DNase I footprinting), a 22-base sequence within this methylated restriction fragment was shown to be specifically protected by MDBP. The sequence-specificity of MDBP coupled with its dependence on DNA methylation suggests that this is one of the proteins which modulates important functions of human DNA methylation in vivo.

The production of generalized transducing phage by bacteriophage lambda

Generalized transduction has for about 30 years been a major tool in the genetic manipulation of bacterial chromosomes. However, throughout that time little progress has been made in understanding how generalized transducing particles are produced. The experiments presented in this paper use phage lambda to assess some of the factors that affect that process. The results of those experiments indicate: the production of generalized transducing particles by bacteriophage lambda is inhibited by the phage lambda exonuclease (Exo). Also inhibited by lambda Exo is the production of lambda docR particles, a class of particles whose packaging is initiated in bacterial DNA and terminated at the normal phage packaging site, cos. In contrast, the production of lambda docL particles, a class of particles whose packaging is initiated at cos and terminated in bacterial DNA, is unaffected by lambda Exo; lambda-generalized transducing particles are not detected in induced lysis-defective (S-) lambda lysogens until about 60-90 min after prophage induction. Since wild-type lambda would normally lyse cells by 60 min, the production of lambda-generalized transducing particles depends on the phage being lysis-defective; if transducing lysates are prepared by phage infection then the frequency of generalized transduction for different bacterial markers varies over a 10-20-fold range. In contrast, if transducing lysates are prepared by the induction of a lambda lysogen containing an excision-defective prophage, then the variation in transduction frequency is much greater, and markers adjacent to, and on both sides of, the prophage are transduced with much higher frequencies than are other markers; if the prophage is replication-defective then the increased transduction of prophage-proximal markers is eliminated; measurements of total DNA in induced lysogens indicate that part of the increase in transduction frequency following prophage induction can be accounted for by an increase in the amount of prophage-proximal bacterial DNA in the cell. Measurements of DNA in transducing particles indicate that the rest of the increase is probably due to the preferential packaging of the prophage-proximal bacterial DNA. These results are most easily interpreted in terms of a model for the initiation of bacterial DNA packaging by lambda, in which the proteins involved (Ter) do not recognize any particular sequence in bacterial DNA but rather recognize some feature of the DNA tht is sensitive to lambda exonuclease, such as a nick or a double-stranded cut.(ABSTRACT TRUNCATED AT 400 WORDS)