Archaea and the prokaryote-to-eukaryote transition

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, Dec. 1997, p. 456–502 1092-2172/97/$04.00 0 Copyright © 1997, American Society for Microbiology

Vol. 61, No. 4

Archaea and the Prokaryote-to-Eukaryote Transition
JAMES R. BROWN1,2*
AND

W. FORD DOOLITTLE1

Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada,1 and Departmentof Bioinformatics, SmithKline Beecham Pharmaceuticals, Collegeville, Pennsylvania2 INTRODUCTION .......................................................................................................................................................457 ARCHAEA ALONE.....................................................................................................................................................457 ARCHAEA AND BACTERIA ......................................................................................................................................458 ARCHAEA AND EUKARYOTES ..............................................................................................................................459 ROOTING THE UNIVERSAL TREE......................................................................................................................460 ACCEPTANCE AND DOUBT...................................................................................................................................461 ORIGIN OF EUKARYOTES ....................................................................................................................................462UNIVERSAL PROTEIN GENE TREES..................................................................................................................465 Methods and Caveats .............................................................................................................................................465 Sequences.............................................................................................................................................................465 Phylogenetic methods .........................................................................................................................................465 Interdomain distance estimates ........................................................................................................................466 DNAReplication and Repair Enzymes................................................................................................................466 DNA gyrases and topoisomerases.....................................................................................................................466 DNA polymeraseB..............................................................................................................................................467 Photolyase ............................................................................................................................................................468 Transcriptional Proteins........................................................................................................................................468Translational Proteins ...........................................................................................................................................469 Elongation factors...............................................................................................................................................470 Aminoacyl-tRNAsynthetases.............................................................................................................................470 Ribosomal proteins.............................................................................................................................................473 Enzymes in Central Metabolism...........................................................................................................................473...