Nucleic Acids Research, Vol 24, Issue 15 2981-2989, Copyright © 1996 by Oxford University Press
R Kaul, M Allen, EM Bradbury and WM Wenman
Chlamydia trachomatis is one of the few prokaryotic organisms known to
contain proteins that bear homology to eukaryotic histone H1. Changes in
macromolecular conformation of DNA mediated by the histone H1-like protein
(Hc1) appear to regulate stage specific differentiation. We have developed
a cross-linking immunoprecipitation protocol to examine in vivo protein-DNA
interaction by immune precipitating chlamydial Hc1 cross linked to DNA. Our
results strongly support the presence of sequence specific binding sites on
the chlamydial plasmid and hc1 gene upstream of its open reading frame. The
preferential binding sites were mapped to 520 bp BamHI-XhoI and 547 bp
BamHI-DraI DNA fragments on the plasmid and hc1 respectively. Comparison of
these two DNA sequences using Bestfit program has identified a 24 bp region
with >75% identity that is unique to the chlamydial genome.
Double-stranded DNA prepared by annealing complementary oligonucleotides
corresponding to the conserved 24 bp region bind Hc1, in contrast to
control sequences with similar A+T ratios. Further, Hc1 binds to DNA in a
strand specific fashion, with preferential binding for only one strand. The
site specific affinity to plasmid DNA was also demonstrated by atomic force
microscopy data images. Binding was always followed by coiling, shrinking
and aggregation of the affected DNA. Very low protein-DNA ratio was
required if incubations were carried out in solution. However, if DNA was
partially immobilized on mica substrate individual strands with dark foci
were still visible even after the addition of excess Hc1.
ARTICLES
Sequence specific binding of chlamydial histone H1-like protein
Department of Pediatrics, University of California, Davis, CA 95616, USA.
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