1. CALCUTT, M.J. AND SCHMIDT, F.J.
Conserved gene arrangement in the origin region of the Streptomyces
J.BACTERIOL. 174 3220-3226 (1992).
2. YEE, T.W. AND SMITH, D.W.
Pseudomonas chromosomal replication origins: a bacterial class distinct
from Escherichia coli-type origins.
PROC.NATL.ACAD.SCI.U.S.A. 87 1278-1282 (1990).
3. SKOVGAARD, O.
Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the
60K-rnpA-rmpH-dnaA-dnaN-recF-gyrB region of Escherichia coli.
GENE 93 27-34 (1990).
Bacterial chromosome replication begins at the origin of replication (oriC),
a target region for many regulatory proteins . The dnaA gene product is
responsible for duplex melting, allowing access to the primosome, which
initiates DNA replication . DnaA binds to conserved 9 base pair repeated
sequences, so-called dnaA boxes, 5 of which are present at oriC [1,2]. DnaA
binding mediates strand opening at three A/T-rich 13 base pair sites,
making them easier to melt . It inhibits its own gene transcription by
feedback inhibition, binding to dnaA boxes in the promoter . The protein
also binds to dnaA boxes in other gene promoters, most of which are
involved in chromosome replication.
The dnaA protein consists of 2 conserved regions: an N-terminal ATP-binding
domain, and a putative DNA-binding region towards the C-terminus . The
protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ
proteins, and the groE gene products (chaperonins) .
DNAA is a 5-element fingerprint that provides a signature for dnaA proteins.
The fingerprint was derived from an initial alignment of 6 sequences: the
motifs were drawn from conserved regions spanning virtually the full
alignment length - motif 1 includes the ATP-binding site, and motif 5
includes the C-terminal DNA-binding region encoded by PROSITE pattern DNAA
(PS01008). Two iterations on OWL24.0 were required to reach convergence, at
which point a true set comprising 14 sequences was identified. Two partial
matches were also found, DNAA_MYCMY and DNAA_SPIAP, both of which are dnaA
An update on SPTR37_9f identified a true set of 33 sequences, and 2