Download Archaebacterial virus SSV1 encodes a putative DnaA

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