Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker

Sandler, S. J., Hugenholtz, P., Schleper, C., DeLong, E. F., Pace, N. R. and Clark, A. J. (1999) Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. Journal of Bacteriology, 181 3: 907-915.

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Author Sandler, S. J.
Hugenholtz, P.
Schleper, C.
DeLong, E. F.
Pace, N. R.
Clark, A. J.
Title Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker
Formatted title
Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker
Journal name Journal of Bacteriology   Check publisher's open access policy
ISSN 0021-9193
1098-5530
Publication date 1999-02-01
Year available 1999
Sub-type Article (original research)
Open Access Status File (Publisher version)
Volume 181
Issue 3
Start page 907
End page 915
Total pages 9
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Language eng
Abstract 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.
Keyword Complete genome sequence
Reca protein
Saccharomyces-cerevisiae
Archaeoglobus-fulgidus
Escherichia-coli
Recombination
Yeast
Homolog
Dmc1
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID AI05371
Institutional Status Unknown

 
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