Bacterias

Article No. jmbi.1999.2827 available online at http://www.idealibrary.com on

J. Mol. Biol. (1999) 289, 729±745

Eukaryotic Signalling Domain Homologues in Archaea and Bacteria. Ancient Ancestry and Horizontal Gene Transfer
C. P. Ponting1*, L. Aravind1, J. Schultz2, P. Bork2 and E. V. Koonin1
National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bldg. 38A, Bethesda MD 20894, USA EMBL, Meyerhofstr. 1 69012 Heidelberg, Germany
2 1

Phyletic distributions of eukaryotic signalling domains were studied using recently developed sensitive methods for protein sequence analysis, with an emphasis on the detection and accurate enumeration of homologues in bacteria and archaea. A major difference was found between the distributions of enzyme families that are typically found in all three divisions of cellular life and non-enzymatic domain families that are usually eukaryote-speci®c. Previously undetected bacterial homologues were identi®ed for# plant pathogenesis-related proteins, Pad1, von Willebrand factor type A, src homology 3 and YWTD repeat-containing domains. Comparisons of the domain distributions in eukaryotes and prokaryotes enabled distinctions to be made between the domains originating prior to the last common ancestor of all known life forms and those apparently originating as consequences of horizontal gene transfer events. A number of transfers of signalling domains from eukaryotes to bacteria were con®dently identi®ed, in contrast to only a single case of apparent transfer from eukaryotes to archaea.
# 1999 Academic Press

*Corresponding author

Keywords: horizontal gene transfer; signalling domains; homology; genome comparison; sequence pro®les

Introduction
Recent genome sequencing of organisms representing each of the three divisions of cellular life (archaea, bacteria and eukaryota) provides opportunities to infer the genetic heritage of the entire set of their genes and portions of genes encoding