The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains

We have investigated the major Escherichia coli histone-like proteins (H-NS , HU, FIS, and IHF) as putative factors involved in the maintenance of the overall DNA looped arrangement of the bacterial nucleoid. The long-range ar chitecture of the chromosome has been studied by means of an assay based on in vivo genomic fragmentation mediated by endogenous DNA gyrase in the pre sence of oxolinic acid. The fragmentation products were analysed by CHEF el ectrophoresis. The results indicate that in vivo a large fraction of the ba cterial chromatin constitutes an adequate substrate for the enzyme. DNA fra gments released upon oxo-treatment span a size range from about 1000 kb to a limit-size of about 50 kb. The latter value is in excellent agreement wit h the average size reported for bacterial chromosomal domains. The DNA gyra se-mediated fragmentation does not appear to be significantly altered in st rains depleted in histone-like proteins as compared to an E. coli wild type strain. This suggests that these proteins may not represent critical deter minants for the maintenance of the supercoiled loop organisation of the E. coli chromosome. (C) 2001 Societe francaise de biochimie et biologie, molec ulaire. / Editions scientifiques et medicales Elsevier SAS. All rights rese rved.