• Arrangement of Dam methylation sites (GATC) in the Escherichia coli chromosome

      Barras, Frederic; Marinus, Martin G. (1988-10-25)
      The occurrence of GATC (Dam-recognition) sites in available E. coli DNA sequences (representing about 2% of the chromosome) has been determined by a simple numerical analysis. Our approach was to analyze the nucleotide composition of nine large sequenced DNA stretches ("cantles") in order to identify patterns of GATC distribution and to rationalize such patterns in biological/structural terms. The following observations were made: (i) In addition to oriC, GATC-rich regions are present in numerous locations. (ii) There is a wide variation in GATC frequency both between and within DNA cantles which led to the identification of a void-cluster pattern of GATC arrangement. The distance between two GATCs was never greater than 2 kb. (iii) GATC sites are found more frequently in translated regions than (in decreasing order) non-coding or non-translated regions. In particular, rRNA and tRNA encoding genes exhibit the lowest GATC content.
    • Genetic Structure of the Bacteriophage P22 P<sub>L</sub> Operon: A Thesis

      Semerjian, Arlene (1989-07-01)
      The sequence of 1360 base pairs of the P22 PL operon was determined, linking a continuous sequence from PL through abc2. P22 mutants bearing deletions in the sequenced region were constructed and tested for their phenotypes. Plasmids were constructed to express PL operon genes singly and in combinations from PlacUV5. Two previously known genes, 17 and c3, are located within this sequence. In addition, three new genes have been identified: ral, kil and arf. Genes ral and c3 are homologous, as well as functionally analogous, to λ ral and cIII, respectively. P22 kil, like λ kil, kills the host cell when it is expressed. The two kil genes, although analogous in cell killing and map location, have no apparent sequence homology. The functions of the P22 and λ kil genes are unknown; however, P22 kil is essential for lytic growth in the absence of abc. Gene arf (accessory recombination function) is located just upstream of erf; it is essential for P22 growth in the absence of kil or other genes upstream in PL. The growth defect of P22 bearing a deletion that removes arf is complemented by expression of either arf or the λ red genes from plasmids. P22 sequences that include the stop codon for 17 potentially form a small stem-loop structure; these sequences are nearly identical to λ sequences that contain the stop codon for ssb. In λ this potential stem-loop structure occupies a map position near the terminator tL2b. Plasmids that include the potential P22 structure negatively regulate kil gene expression in cis.