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Nucleic Acids Research, Vol. 20, No. 5 1143 Archaebacterial virus SSV1 encodes a putative DnaA-like protein Eugene V.Koonin* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Submitted January 2, 1992 In a previous study (1) we have shown that proteins containing the purine NTP-binding sequence pattern (2) and involved in genome replication or DNA precursor synthesis are extremely wide-spread products of the genomes of various viruses. In particular, all viruses with double-stranded (ds) DNA genomes, for which complete sequences were available at the time, have been shown to encode at least one protein of this class. All these viruses reproduce either in eubacterial, or in eucaryotic cells. Recently two sequences of dsDNA viruses of Archaebacteria, SSV1 of Sulfolobus shibatae and TTV1 of Thermoproteus tenax, became available (3, 4). It was of interest to find out whether these viruses also encoded NTP-binding pattern-containing proteins. Search of the protein sequences encoded by the two archaebacteria] viruses showed that TTV1 did not encode proteins of this type. On the contrary, SSV1 protein B251 contained clearly defined motifs 'A' and 'B' that together constitute the NTP-binding pattern. Screening the non-redundant amino acid sequence data base (National Center for Biotechnology Information) with the B251 sequence using the BLASTP program (5) failed to reveal close similarities. However, a detailed search for local similarity with NTP-binding pattern-containing proteins using the program DOTHELJX (6) detected a moderate but significant similarity with bacterial DnaA proteins. Multiple alignment of the D251 sequence with the DnaA sequences was generated using the program OPTAL (7) and scored 6.3 standard deviafions over the random expectation. Its inspection revealed identical spacing of the 'A' and 'B' motifs and a number of additional coincidences between the SSV1 protein and DnaA proteins (Figure). Screening of the data base with DnaA sequences revealed also an additional member of the emerging family of DnaA-related proteins, the product of an unassigned reading frame (ORF 311) adjacent to the DnaB gene of Bacillus subtilis (Figure; ref. 8). DnaA is a multifunctional protein which binds to specific sites in bacterial DNA and ensures both replication initiation and regulation of transcription of specific genes in an ATP-dependent manner, basically by promoting local unwinding of dsDNA (9, 10). Both functions are plausible for B251 protein in SSV1 reproduction. This analysis showed that i) an archaebacterial virus, SSV 1, encodes a putative DnaA-related ATPase; ii) a dsDNA virus (TTVI) does not encode NTP-binding pattern-containing proteins, and iii) in addition to the bona fide DnaA, Bacillus subtilis encodes a DnaA-related protein of unknown function. REFERENCES 1. Gorbalenya.A.E. and Koonin.E.V. (1989) Nucleic Acids Res. 17, 8413-8440. 2. WalkerJ.E., el ai. (1982) EMBO J. 1, 945-951. 3. Palm.P., el al. (1991) Virology 185, 242-250. 4. Neumann.H., et al. (1989) Mol. Gen. Genet. 217, 105-110. 5. Altschul.S.F., et al. (1990) J. Mol. Biol. 215, 403-410. 6. Leontovich.A.M., et al. (1990) Biopolimeri i Kletka 6, 14-21 (in Russian). 7. Gorbalenya.A.E., et al. (1989) J. Mol. Evol. 28, 256-268. Ogasawara.N., et al. (1986) Nucleic Acids Res. 14, 9989-9999. McMacken.R., et al. (1987) In Escherichia coli and Salmonella typhimurium, Neidhardt.F.C, Ingraham.J.L., Low.K.B , Magasanik, B., Schaechter.M. and Umbarger.H.E. (eds), ASM, Washington, DC, pp. 564-612. 10 Georgopoulos.C. (1989) Trends Genet. 5, 219-221. 15-34IS-J4- Mil omi OB MTVJXVTLttt anrtoanrniTOMn IM* list t m uwnjmtoaxrniTaiaaivwctaTJ-rtnDi-UTTKii—< Alignment of the amino acid sequences of bacterial DnaA proteins, B251 ORF product of SSV 1 and ORF 311 product of Bacillus subtilis. The boundaries of the aligned segments in each protein are indicated in parentheses. Asterisks denote identical, and colons similar amino acid residues in B251 and at least five out of six DnaA proteins, or in B251 and ORF 311 protein. Exclamation marks — identical or similar residues in all aligned sequences. The following groups of similar residues were considered: 1) G,A; 2) S,T; 3) D,E,N,Q; 4) K,R; 5) I,L.V,M: 6) F,Y,W. The two sequence motifs constituting the NTP-binding pattern are delineated. E.c, — E.coii, P.m. — Proteus mirabilis. P.p. — Pseudomonas putida, M.c. — Mycoplasma capricoli, B.s. — Bacillus subtilis, M.I. — Micrococcus luteus. The sequences were from P1R protein sequence bank (Release 30.0). •On leave from Institute of Microbiology, Academy of Sciences, 117811 Moscow, Russia