Sequence Periodicity in Complete Genomes of Archaea
Suggests Positive Supercoiling
Hanspeter Herzel1*,
Olaf Weiss1
and Edward N. Trifonov2
1Institute for Theoretical Biology,
Humboldt University, Invalidenstr. 43,
10115 Berlin, Germany
2Department of Structural Biology,
Weizmann Institute of Science,
Rehovot 76100, Israel
*Author to whom correspondence should be addressed.
Phone: +49 30 2093; Fax: +49 30 2093-8801; E-mail:
h.herzel@biologie.huberlin.de
Journal of Biomolecular Structure & Dynamics
16(2), 341-345 (October 1998)
Abstract
The topological state of genomic DNA is of importance for its
replication, recombination and transcription. The wrapping of
the DNA around nucleosomes is associated with sequence periodicities
(Trifonov and Sussman, Proc. Natl. Acad. Sci. USA, 77, pp. 3816-20).
Recently, also the negative supercoiling of eubacterial DNA was
related to 11 base pair (bp) periodicity (Herzel et al. Physica A,
249, pp. 449-59). Archaeal plasmids and a virus-like particle
from Sulfolobus are positively supercoiled, but the superhelical
conformation of archaeal genomic DNA is still uncertain. The
problem of superhelicity can now be addressed via a comparative
statistical analysis of the available complete genomes. For this
purpose one has to look for periodicities which are in phase with
the helical repeat of 10-11 bp. Similar periodicities are induced,
however, by the amphipatic character of alpha-helices of encoded
proteins (Zhurkin, Nucl. Acids Res., 9, pp.
1963-71).
We show that these protein-induced periodicities are extended over
a few periods only. The periods of additional long-ranging
oscillations deviate significantly from the value for free
DNA. A period of 11 bp in Eubacteria reflects negative supercoiling,
whereas the significantly different period of thermophilic Archaea
close to 10 bp suggests positive supercoiling of archaeal genomes.
