Nucleic Acids Research, Vol 27, Issue 5 1223-1242, Copyright © 1999 by Oxford University Press
L Aravind, DR Walker and EV Koonin
A detailed analysis of protein domains involved in DNA repair was performed
by comparing the sequences of the repair proteins from two well-studied
model organisms, the bacterium Escherichia coli and yeast Saccharomyces
cerevisiae, to the entire sets of protein sequences encoded in completely
sequenced genomes of bacteria, archaea and eukaryotes. Previously
uncharacterized conserved domains involved in repair were identified,
namely four families of nucleases and a family of eukaryotic repair
proteins related to the proliferating cell nuclear antigen. In addition, a
number of previously undetected occurrences of known conserved domains were
detected; for example, a modified helix- hairpin-helix nucleic acid-binding
domain in archaeal and eukaryotic RecA homologs. There is a limited
repertoire of conserved domains, primarily ATPases and nucleases, nucleic
acid-binding domains and adaptor (protein-protein interaction) domains that
comprise the repair machinery in all cells, but very few of the repair
proteins are represented by orthologs with conserved domain architecture
across the three superkingdoms of life. Both the external environment of an
organism and the internal environment of the cell, such as the chromatin
superstructure in eukaryotes, seem to have a profound effect on the layout
of the repair systems. Another factor that apparently has made a major
contribution to the composition of the repair machinery is horizontal gene
transfer, particularly the invasion of eukaryotic genomes by organellar
genes, but also a number of likely transfer events between bacteria and
archaea. Several additional general trends in the evolution of repair
proteins were noticed; in particular, multiple, independent fusions of
helicase and nuclease domains, and independent inactivation of enzymatic
domains that apparently retain adaptor or regulatory functions.
REVIEWS
Conserved domains in DNA repair proteins and evolution of repair systems
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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