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Strawberry Vein Banding Virus—Definitive Member of the Genus Caulimovirus

Article  in  Virus Genes · February 1998

DOI: 10.1023/A:1008039024963 · Source: PubMed

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 Virus Genes 16:3, 303±305, 1998
# 1998 Kluwer Academic Publishers, Boston. Manufactured in The Netherlands.

Strawberry Vein Banding VirusÐDe®nitive Member of the

Genus Caulimovirus

 2 IVAN MRA
KAREL PETRZIK,1* VLADIMIR BENES, Â Z,1 JANA HONETSLEGROVA
 Â -FRA
 NOVA
 ,1
2
WILHELM ANSORGE & JOSEF SPAK  1

1
sovska 31, CZ-370 05,
Department of Virology, Institute of Plant Molecular Biology, Academy of Sciences of the Czech Republic, Brani
 Â Bud
Ceske ejovice, Czech Republic, E-mail: petrzik@umbr.cas.cz 2EMBL, Meyerhofstraûe 1, D-69117 Heidelberg, Germany

Received November 10, 1997; Accepted January 11, 1998

Abstract. The complete DNA sequence (7876 nucleotides) of strawberry vein banding virus (SVBV) has been
determined. Seven open reading frames are detected that potentially code for proteins of calculated weight 37.8;
18.3; 16.6; 56.0; 81.1; 59.0 and 12.6 kDa, respectively. Their position on the viral genome is the same as that of the
corresponding proteins on the cauli¯ower mosaic virus (CaMV) genome. Phylogenetic analysis based on the
amino acid sequence of this protein shows a closer relationship of SVBV with CaMV, ®gwort mosaic virus and
carnation etched ring virus than with other caulimoviruses.

Key words: complete DNA sequence, phylogenetic relationship, protein comparison, strawberry vein
banding virus

Introduction Materials and Methods

The strawberry vein banding disease of cultivated
strawberries has been known for several decades (1),
but it is only in the 1980s that its causal agent was
shown to be a virus, strawberry vein banding virus
(SVBV) (2). The virus is transmitted by grafting or by
aphids in a semipersistent manner (3) and is probably
distributed world-wide on cultivated strawberries.
Weak serological relationship with CaMV was
reported (4,5). The double-stranded DNA nature of
the viral genome was established and the genome was
mapped with restriction endonucleases (6). SVBV has
a 7.8 kbp circular dsDNA genome with one single-
stranded discontinuity on each DNA strand. Due to
the previous absence of any sequencing data, the
virus had been classi®ed as a tentative member of
the Caulimoviridae (7). In this paper we report the
complete nucleotide sequence of SVBV and compare
it with the sequences of previously characterized
caulimoviruses.
*Corresponding author
A full-length clone pSVBV-E3 (6) was digested with
HindIII and subcloned into pUC18. Double stranded
DNA templates were cycle sequenced using the
Thermo sequenase cycle sequencing kit (Amersham,
England) with the ¯uorescein- (Pharmacia, Uppsala,
Sweden) and Texas red-labeled (Genosys, Cambridge,
England) M13±20, and M13 reverse sequencing
primers. Sequencing was performed on an automated
A.L.F. DNA sequencer (Pharmacia, Uppsala,
Sweden). Sequencing data were analyzed on the
GeneSkipper programme (EMBL, Heidelberg,
Germany), and the phylogenetic tree was built by
UPGMA method (8).
Results and Discussion
The complete sequence of the ( ‡ ) strand of SVBV
DNA (GenBank nucleotide sequence database acces-
sion number X97304) comprises 7876 bp and differs
from the other caulimoviruses by the presence of
only two single-stranded discontinuities (G1 and
304 Petrzik et al.
G2Ðmarked according to (6)). We located the G2 gap
just upstream of nucleotide position 1, and G1 near
position 3828, where a purine-rich region (9,10) is
observed.
Computer analysis revealed seven putative open
reading frames (ORFs) for proteins longer than
10 kDa on the ( ‡ ) strand and no ORF coding for
proteins 4 10 kDa on the complementary strand (Fig.
1). ORF VII and ORF I±IV are contiguous as well as
ORF V and VI. The arrangement of the ORFs is hence
very similar to that of CaMV (9) with the exception of
the position of the small noncoding region between
ORF IV and V.
If the transcription strategy of SVBV is similar to
that of CaMV which uses a separate transcript for
ORF VI, two promoters should be present on the
genome. Eight potential promoter regions each
containing a TATA box can be detected (Fig. 1).
Among them, the TATATAA sequence at position
7220 located within the large intergenic region is the
only one to be preceded by GTGG enhancer signals by
distances similar to the ones present in CaMV. In
addition, the poly-A termination signal begins at
position 7325, leading us to suppose that this region
probably represents the main promoter of the virus
genome as it does in the CaMV genome.
Fig. 1. Organization of the SVBV genome. Open arrows indicate
the position of the ORFs. G1 and G2 (closed circles) correspond
to the position of the single-stranded discontinuities. The black
triangles indicate potential TATA boxes, open triangles potential
transcriptional GTGGA/T enhancer signals and open circle the
termination poly-A signal. The region of the putative main
promoter is marked by a hatched box.
There is no TATA-like box in the small intergenic
region, the closest TATAAAT sequence preceding the
initiator ATG of ORF V being about 210 bp upstream.
This is unlike the situation in ®gwort mosaic virus
(FMV) and carnation etched ring virus (CERV),
where the TATA box precedes the ®rst ATG of the
separately expressed ORF VI by 70 and 38 bp,
respectively (9,11).
The SVBV genome can potentially code for seven
proteins of calculated weight 37.8, 18.3; 16.6; 56.0;
81.1; 59.0 and 12.6 kDa. Despite the remarkable
similarity of the arrangement of these ORFs to those
of CaMV, FMV and CERV, only low similarity exists
between the amino acid sequences of the corre-
sponding ORFs. With the exception of ORF V of
SVBV which presents more than 50% homology with
ORF V of FMV, the other proteins share only about
20% homology with the other caulimo-encoded
proteins.
The product of ORF I is believed to be involved in
cell-to-cell movement. Indeed, amino acid homology
with the 30 K movement protein of tobacco mosaic
virus was found in the region starting with amino acid
140 in SVBV. In addition, two other domains
conserved among caulimoviruses are located at
amino acid positions 161±167 and 216±224.
The postulated function of protein encoded by
ORF II is in aphid transmission. This protein has a
very high Leu content (12.4%) and is the most basic
protein of SVBV (calculated pI 8.43).
ORF III is a non-sequence speci®c DNA-binding
protein in CaMV (12). No conserved motif can be
detected in this protein. In the C-terminal part of the
protein, where CaMV, CERV and FMV harbor the
conserved motif VGNExxGSS (amino acids are
presented in the single letter code, x denotes any
amino acid), SVBV possesses the LAHKxxSPK
sequence.
ORF IV encodes the viral coat protein. It contains
at amino acid position 399±412 the conserved zinc-
®nger domain with the arrangement Cx2Cx4Hx4C
typical of the coat protein of all the caulimoviruses.
The predicted size of the protein is slightly higher than
that determined by SDS-acrylamide gel electrophor-
esis of the viral particles (48 kDa) (5), and agrees with
the assumption that the coat protein is produced as a
precursor and undergoes posttranslational cleavage.
Based on the comparison of SVBV with CaMV
(53.4% amino acid identity), ORF V codes for the
replicase. All four motifs of this multifunctional

protein are present in SVBV: a Leu-zip motif near the
N-terminus, an Asp-proteinase domain between
amino acids 78 and 86, a reverse transcriptase
domain between amino acids 433 and 442, and an
RNase-H domain between amino acids 583 and 695
(13).
The protein encoded by ORF VI is similar to the
CaMV transactivator protein and probably controls
virus-host speci®city. A short conserved sequence
P 5 9 4 GLxxIY reported to be conserved in the
other caulimoviruses (14) is found between amino
acids 297 and 315.
No reliable degree of homology can be detected
between protein encoded by ORF VII and proteins
contained in the GenBank database. In CaMV it plays
a role in translational transactivation (15).
A phylogenetic analysis carried out on the amino
acid sequence of the ORF V of SVBV, CaMV, CERV,
FMV, soybean chlorotic mottle virus (SoyCMV) and
peanut chlorotic streak virus (PCSV) reveals that
these six caulimoviruses form two groups: SVBV
shows close relationship to CaMV, FMV and CERV,
while the other group links PCSV and SoyCMV.
The data reported here allows us to de®nitively
place SVBV into the plant virus genus Caulimovirus.
Two discontinuities on the circular dsDNA genome
and the identi®cation of one caulimo-like promoter
raise new questions about replication and transcrip-
tion of the viral proteins. Analogy between the main
promoter in SVBV and the 35S promoter of CaMV,
together with the restricted host range of SVBV
should be promising for future use in the transforma-
tion of many Rosaceae plants in culture.
Acknowledgments
The authors thank J. Postman (USDA, ARS, HRCL,
Corvallis, Oregon, USA) for kindly providing the
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Strawberry Vein Banding Virus 305
SVBV clone. This work was supported by the Grant
Agency of the Czech Republic, no. 522/96/0854 and
the COST 823 project of the EC.
References
1. Frazier N.W., Phytopathology 45, 307±312, 1995.
2. Frazier N.W. and Morris T.J., in Converse R.H. (ed.) Virus
diseases of small fruits. US Department of Agriculture,
Corvallis, Oregon, 1987, pp. 16±20.
3. Frazier N.W. and Converse R.F., Description of Plant Viruses,
CMI and AAB, Kew, Surrey, England, 1980, No. 219.
4. Morris T.J., Mullin R.H., Schlegel D.E., Cole A., and Alosi
M.C., Phytopathology 70, 156±160, 1980.

5. Honetslegrova J., MraÂz I., and Spak J., Acta Horticulturae 385,
29±32, 1995.
6. Stenger D.C., Mullin R.H., and Morris T.J., Phytopathology 78,
154±159, 1988.
7. Brunt A.A., Crabtree K., Dallwitz M.J., Gibbs A.J., Watson L.,
and Zurcher E.J. (eds) Plant Viruses Online: Descriptions and
Lists from the VIDE Database, 1996, Version: 16th January
1997.
8. Sneath P.H.A. and Sokal R.R., Numerical taxonomy. W.H.
Freeman, New York, 1973.
9. Hull R., Sadler J., and Longstaff M., EMBO J 5, 3083±3090,
1986.
10. Franck A., Guilley H., Jonard G., Richard K., and Hirth L., Cell
21, 285±294, 1980.
11. Richins R.D., Scholthof H.B., and Shepherd R.J., Nucleic Acids
Res 15, 8451±8466, 1987.
12. Mesnard J.-M., Kirchherr D., Wurch T., and Lebeurier G.,
Virology 174, 622±624, 1990.
13. Hay J.M., Jones M.C., Blakebrough M.L., Dasgupta I., Davies
J.W., and Hull R., Nucleic Acids Res 19, 2615±2621, 1991.
14. Hasegawa A.J., Verver A., Shimada A., Saito M., Goldbach R.,
Van Kammen A., Miki K., Kameya-Iwaki M., and Hibi T.,
Nucleic Acids Res 17, 9993±10013, 1989.
15. FuÈtterer J., Kiss-Laszlo Z., and Hohn T., Cell 73, 789±802,
1993.