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Journal of Bacteriology, February 1999, p. 907-915, Vol. 181, No. 3
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Diversity of radA Genes from Cultured and Uncultured Archaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

Steven J. Sandler,1,dagger Philip Hugenholtz,2 Christa Schleper,3 Edward F. DeLong,3,Dagger Norman R. Pace,1,2 and Alvin J. Clark1,*

Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-32021; Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-31022; and Marine Science Institute, University of California, Santa Barbara, California 931063

Received 8 June 1998/Accepted 20 November 1998

Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of Crenarcheota. The two most deeply branching archaeal radA genes found had some amino acid deletion and insertion patterns characteristic of bacterial recA genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members.

* Corresponding author. Present address: Lawrence Berkeley National Laboratory, Life Science Division, 1 Cyclotron Road, Building 74-157, Berkeley, CA 94720. Phone: (510) 486-5196. Fax: (510) 486-6690. E-mail: AJClark{at}LBL.gov.

dagger Present address: Department of Microbiology, University of Massachusetts, Amherst, MA 01003.

Dagger Present address: Monterey Bay Aquarium Institute, Moss Landing, CA 95039.

Journal of Bacteriology, February 1999, p. 907-915, Vol. 181, No. 3
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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