Abstract
The process of homologous recombination has been documented in bacterial and eucaryotic organisms. The Escherichia coli RecA and Saccharomyces cerevisiae Rad51 proteins are the archetypal members of two related families of proteins that play a central role in this process. Using the PCR process primed by degenerate oligonucleotides designed to encode regions of the proteins showing the greatest degree of identity, we examined DNA from three organisms of a third phylogenetically divergent group, Archaea, for sequences encoding proteins similar to RecA and Rad51. The archaeans examined were a hyperthermophilic acidophile, Sulfolobus sofataricus (Sso); a halophile, Haloferax volcanii (Hvo); and a hyperthermophilic piezophilic methanogen, Methanococcus jannaschii (Mja). The PCR generated DNA was used to clone a larger genomic DNA fragment containing an open reading frame (orf), that we refer to as the radA gene, for each of the three archaeans. As shown by amino acid sequence alignments, percent amino acid identities and phylogenetic analysis, the putative proteins encoded by all three are related to each other and to both the RecA and Rad51 families of proteins. The putative RadA proteins are more similar to the Rad51 family (approximately 40% identity at the amino acid level) than to the RecA family (approximately 20%). Conserved sequence motifs, putative tertiary structures and phylogenetic analysis implied by the alignment are discussed. The 5' ends of mRNA transcripts to the Sso radA were mapped. The levels of radA mRNA do not increase after treatment with UV irradiation as do recA and RAD51 transcripts in E.coli and S.cerevisiae. Hence it is likely that radA in this organism is a constitutively expressed gene and we discuss possible implications of the lack of UV-inducibility.
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- Akaboshi E., Inoue Y., Ryo H. Cloning of the cDNA and genomic DNA that correspond to the recA-like gene of Drosophila melanogaster. Jpn J Genet. 1994 Dec;69(6):663–670. doi: 10.1266/jjg.69.663. [DOI] [PubMed] [Google Scholar]
- Bachmann B. J., Low K. B. Linkage map of Escherichia coli K-12, edition 6. Microbiol Rev. 1980 Mar;44(1):1–56. doi: 10.1128/mr.44.1.1-56.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Basile G., Aker M., Mortimer R. K. Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51. Mol Cell Biol. 1992 Jul;12(7):3235–3246. doi: 10.1128/mcb.12.7.3235. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Baumann P., Qureshi S. A., Jackson S. P. Transcription: new insights from studies on Archaea. Trends Genet. 1995 Jul;11(7):279–283. doi: 10.1016/s0168-9525(00)89075-7. [DOI] [PubMed] [Google Scholar]
- Benedict R. C., Kowalczykowski S. C. Increase of the DNA strand assimilation activity of recA protein by removal of the C terminus and structure-function studies of the resulting protein fragment. J Biol Chem. 1988 Oct 25;263(30):15513–15520. [PubMed] [Google Scholar]
- Bezzubova O., Shinohara A., Mueller R. G., Ogawa H., Buerstedde J. M. A chicken RAD51 homologue is expressed at high levels in lymphoid and reproductive organs. Nucleic Acids Res. 1993 Apr 11;21(7):1577–1580. doi: 10.1093/nar/21.7.1577. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bishop D. K., Park D., Xu L., Kleckner N. DMC1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell. 1992 May 1;69(3):439–456. doi: 10.1016/0092-8674(92)90446-j. [DOI] [PubMed] [Google Scholar]
- Bishop D. K. RecA homologs Dmc1 and Rad51 interact to form multiple nuclear complexes prior to meiotic chromosome synapsis. Cell. 1994 Dec 16;79(6):1081–1092. doi: 10.1016/0092-8674(94)90038-8. [DOI] [PubMed] [Google Scholar]
- Brock T. D., Brock K. M., Belly R. T., Weiss R. L. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol. 1972;84(1):54–68. doi: 10.1007/BF00408082. [DOI] [PubMed] [Google Scholar]
- Brown J. R., Doolittle W. F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci U S A. 1995 Mar 28;92(7):2441–2445. doi: 10.1073/pnas.92.7.2441. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Camerini-Otero R. D., Hsieh P. Homologous recombination proteins in prokaryotes and eukaryotes. Annu Rev Genet. 1995;29:509–552. doi: 10.1146/annurev.ge.29.120195.002453. [DOI] [PubMed] [Google Scholar]
- Cheng R., Baker T. I., Cords C. E., Radloff R. J. mei-3, a recombination and repair gene of Neurospora crassa, encodes a RecA-like protein. Mutat Res. 1993 Oct;294(3):223–234. doi: 10.1016/0921-8777(93)90005-2. [DOI] [PubMed] [Google Scholar]
- Clark A. J., Satin L., Chu C. C. Transcription of the Escherichia coli recE gene from a promoter in Tn5 and IS50. J Bacteriol. 1994 Nov;176(22):7024–7031. doi: 10.1128/jb.176.22.7024-7031.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cole G. M., Mortimer R. K. Failure to induce a DNA repair gene, RAD54, in Saccharomyces cerevisiae does not affect DNA repair or recombination phenotypes. Mol Cell Biol. 1989 Aug;9(8):3314–3322. doi: 10.1128/mcb.9.8.3314. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gogarten J. P., Kibak H., Dittrich P., Taiz L., Bowman E. J., Bowman B. J., Manolson M. F., Poole R. J., Date T., Oshima T. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6661–6665. doi: 10.1073/pnas.86.17.6661. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grogan D. W., Gunsalus R. P. Sulfolobus acidocaldarius synthesizes UMP via a standard de novo pathway: results of biochemical-genetic study. J Bacteriol. 1993 Mar;175(5):1500–1507. doi: 10.1128/jb.175.5.1500-1507.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gupta R., Lanter J. M., Woese C. R. Sequence of the 16S Ribosomal RNA from Halobacterium volcanii, an Archaebacterium. Science. 1983 Aug 12;221(4611):656–659. doi: 10.1126/science.221.4611.656. [DOI] [PubMed] [Google Scholar]
- Haaf T., Golub E. I., Reddy G., Radding C. M., Ward D. C. Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):2298–2302. doi: 10.1073/pnas.92.6.2298. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hain J., Reiter W. D., Hüdepohl U., Zillig W. Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids Res. 1992 Oct 25;20(20):5423–5428. doi: 10.1093/nar/20.20.5423. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hays S. L., Firmenich A. A., Berg P. Complex formation in yeast double-strand break repair: participation of Rad51, Rad52, Rad55, and Rad57 proteins. Proc Natl Acad Sci U S A. 1995 Jul 18;92(15):6925–6929. doi: 10.1073/pnas.92.15.6925. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Iwabe N., Kuma K., Hasegawa M., Osawa S., Miyata T. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9355–9359. doi: 10.1073/pnas.86.23.9355. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jang Y. K., Jin Y. H., Kim E. M., Fabre F., Hong S. H., Park S. D. Cloning and sequence analysis of rhp51+, a Schizosaccharomyces pombe homolog of the Saccharomyces cerevisiae RAD51 gene. Gene. 1994 May 16;142(2):207–211. doi: 10.1016/0378-1119(94)90262-3. [DOI] [PubMed] [Google Scholar]
- Johnson R. D., Symington L. S. Functional differences and interactions among the putative RecA homologs Rad51, Rad55, and Rad57. Mol Cell Biol. 1995 Sep;15(9):4843–4850. doi: 10.1128/mcb.15.9.4843. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jones J. G., Young D. C., DasSarma S. Structure and organization of the gas vesicle gene cluster on the Halobacterium halobium plasmid pNRC100. Gene. 1991 Jun 15;102(1):117–122. doi: 10.1016/0378-1119(91)90549-q. [DOI] [PubMed] [Google Scholar]
- Kans J. A., Mortimer R. K. Nucleotide sequence of the RAD57 gene of Saccharomyces cerevisiae. Gene. 1991 Aug 30;105(1):139–140. doi: 10.1016/0378-1119(91)90527-i. [DOI] [PubMed] [Google Scholar]
- Karlin S., Brocchieri L. Evolutionary conservation of RecA genes in relation to protein structure and function. J Bacteriol. 1996 Apr;178(7):1881–1894. doi: 10.1128/jb.178.7.1881-1894.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karlin S., Weinstock G. M., Brendel V. Bacterial classifications derived from recA protein sequence comparisons. J Bacteriol. 1995 Dec;177(23):6881–6893. doi: 10.1128/jb.177.23.6881-6893.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kobayashi T., Hotta Y., Tabata S. Isolation and characterization of a yeast gene that is homologous with a meiosis-specific cDNA from a plant. Mol Gen Genet. 1993 Feb;237(1-2):225–232. doi: 10.1007/BF00282804. [DOI] [PubMed] [Google Scholar]
- Kobayashi T., Kobayashi E., Sato S., Hotta Y., Miyajima N., Tanaka A., Tabata S. Characterization of cDNAs induced in meiotic prophase in lily microsporocytes. DNA Res. 1994;1(1):15–26. doi: 10.1093/dnares/1.1.15. [DOI] [PubMed] [Google Scholar]
- Kowalczykowski S. C., Dixon D. A., Eggleston A. K., Lauder S. D., Rehrauer W. M. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994 Sep;58(3):401–465. doi: 10.1128/mr.58.3.401-465.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kowalczykowski S. C., Eggleston A. K. Homologous pairing and DNA strand-exchange proteins. Annu Rev Biochem. 1994;63:991–1043. doi: 10.1146/annurev.bi.63.070194.005015. [DOI] [PubMed] [Google Scholar]
- Lovett S. T. Sequence of the RAD55 gene of Saccharomyces cerevisiae: similarity of RAD55 to prokaryotic RecA and other RecA-like proteins. Gene. 1994 May 3;142(1):103–106. doi: 10.1016/0378-1119(94)90362-x. [DOI] [PubMed] [Google Scholar]
- Maeshima K., Morimatsu K., Shinohara A., Horii T. RAD51 homologues in Xenopus laevis: two distinct genes are highly expressed in ovary and testis. Gene. 1995 Jul 28;160(2):195–200. doi: 10.1016/0378-1119(95)00148-y. [DOI] [PubMed] [Google Scholar]
- Miller J. F., Shah N. N., Nelson C. M., Ludlow J. M., Clark D. S. Pressure and Temperature Effects on Growth and Methane Production of the Extreme Thermophile Methanococcus jannaschii. Appl Environ Microbiol. 1988 Dec;54(12):3039–3042. doi: 10.1128/aem.54.12.3039-3042.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Morita T., Yoshimura Y., Yamamoto A., Murata K., Mori M., Yamamoto H., Matsushiro A. A mouse homolog of the Escherichia coli recA and Saccharomyces cerevisiae RAD51 genes. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6577–6580. doi: 10.1073/pnas.90.14.6577. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Muris D. F., Vreeken K., Carr A. M., Broughton B. C., Lehmann A. R., Lohman P. H., Pastink A. Cloning the RAD51 homologue of Schizosaccharomyces pombe. Nucleic Acids Res. 1993 Sep 25;21(19):4586–4591. doi: 10.1093/nar/21.19.4586. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ogawa T., Yu X., Shinohara A., Egelman E. H. Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science. 1993 Mar 26;259(5103):1896–1899. doi: 10.1126/science.8456314. [DOI] [PubMed] [Google Scholar]
- Olsen G. J., Pace N. R., Nuell M., Kaine B. P., Gupta R., Woese C. R. Sequence of the 16S rRNA gene from the thermoacidophilic archaebacterium Sulfolobus solfataricus and its evolutionary implications. J Mol Evol. 1985;22(4):301–307. doi: 10.1007/BF02115685. [DOI] [PubMed] [Google Scholar]
- Palm P., Schleper C., Grampp B., Yeats S., McWilliam P., Reiter W. D., Zillig W. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology. 1991 Nov;185(1):242–250. doi: 10.1016/0042-6822(91)90771-3. [DOI] [PubMed] [Google Scholar]
- Palmer J. R., Daniels C. J. In vivo definition of an archaeal promoter. J Bacteriol. 1995 Apr;177(7):1844–1849. doi: 10.1128/jb.177.7.1844-1849.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roca A. I., Cox M. M. The RecA protein: structure and function. Crit Rev Biochem Mol Biol. 1990;25(6):415–456. doi: 10.3109/10409239009090617. [DOI] [PubMed] [Google Scholar]
- Scoarughi G. L., Cimmino C., Donini P. Lack of production of (p)ppGpp in Halobacterium volcanii under conditions that are effective in the eubacteria. J Bacteriol. 1995 Jan;177(1):82–85. doi: 10.1128/jb.177.1.82-85.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shinohara A., Ogawa H., Matsuda Y., Ushio N., Ikeo K., Ogawa T. Cloning of human, mouse and fission yeast recombination genes homologous to RAD51 and recA. Nat Genet. 1993 Jul;4(3):239–243. doi: 10.1038/ng0793-239. [DOI] [PubMed] [Google Scholar]
- Shinohara A., Ogawa H., Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell. 1992 May 1;69(3):457–470. doi: 10.1016/0092-8674(92)90447-k. [DOI] [PubMed] [Google Scholar]
- Story R. M., Bishop D. K., Kleckner N., Steitz T. A. Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast. Science. 1993 Mar 26;259(5103):1892–1896. doi: 10.1126/science.8456313. [DOI] [PubMed] [Google Scholar]
- Story R. M., Steitz T. A. Structure of the recA protein-ADP complex. Nature. 1992 Jan 23;355(6358):374–376. doi: 10.1038/355374a0. [DOI] [PubMed] [Google Scholar]
- Story R. M., Weber I. T., Steitz T. A. The structure of the E. coli recA protein monomer and polymer. Nature. 1992 Jan 23;355(6358):318–325. doi: 10.1038/355318a0. [DOI] [PubMed] [Google Scholar]
- Sung P., Robberson D. L. DNA strand exchange mediated by a RAD51-ssDNA nucleoprotein filament with polarity opposite to that of RecA. Cell. 1995 Aug 11;82(3):453–461. doi: 10.1016/0092-8674(95)90434-4. [DOI] [PubMed] [Google Scholar]
- White C. I., Haber J. E. Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. EMBO J. 1990 Mar;9(3):663–673. doi: 10.1002/j.1460-2075.1990.tb08158.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zillig W., Palm P., Reiter W. D., Gropp F., Pühler G., Klenk H. P. Comparative evaluation of gene expression in archaebacteria. Eur J Biochem. 1988 May 2;173(3):473–482. doi: 10.1111/j.1432-1033.1988.tb14023.x. [DOI] [PubMed] [Google Scholar]