Download Nucleotide sequences of genome segments $8, encoding a capsid

Journal of General Virology (1991), 72, 2837-2842. Printed in Great Britain
2837
Nucleotide sequences of genome segments $8, encoding a capsid protein,
and $10, encoding a 36K protein, of rice gall dwarf virus
Hiroaki Noda, 1 Koichi Ishikawa, 2 Hiroyuki Hibino, 2 Hajime Kato2t and Toshihiro Omura 2.
1National Institute of Sericultural and Entomological Science and 2National Agriculture Research Center, Tsukuba,
Ibaraki 305, Japan
The nucleotide sequences of DNAs complementary to
the eighth ($8) and the tenth (S10) largest of the 12
genome segments of rice gall dwarf virus (RGDV) were
determined. The $8 and S10 segments consist of 1578
and 1198 nucleotides, each with a single open reading
frame extending for 1278 nucleotides from nucleotide
21, and 960 nucleotides from nucleotide 22, respectively. $8 encodes a polypeptide of 426 amino acids with
an Mr of 47419. The amino acid sequences of several
peptide fragments of the major outer capsid protein
reported as 45K were contained in the predicted
polypeptide. This protein, renamed the 47K protein,
showed high homology with the outer capsid proteins
of rice dwarf virus (RDV) and wound tumour virus
(WTV); there was 56, 52 and 48 % amino acid sequence
identity between R G D V and WTV, R G D V and RDV,
and R D V and WTV, respectively. S10 had the coding
potential for a polypeptide of 320 amino acids with an
Mr of 36095 (36K protein), which exhibits 32% and
35 % amino acid sequence identity with the predicted
translation product of R D V $9 and the P9 capsid
protein encoded by WTV S 1 l, respectively. The
conserved terminal sequences 5' G G . . . G A U 3' which
are present in all genome segments of W T V and R D V
so far analysed, and in $9 of RGDV, were also found in
R G D V $8 and S 10. This conserved sequence together
with the segment-specific inverted repeats found in the
terminal sequence of R G D V $8 and S10 are thus
characteristic structures common to all three phytoreoviruses. The nucleotide sequence of the region surrounding the inverted repeats was more similar
between R G D V and WTV than between R G D V and
RDV.
The phytoreoviruses, wound tumour virus (WTV), rice
dwarf virus (RDV) and rice gall dwarf virus (RGDV),
have icosahedral double-shelled particles approximately
65 to 70 nm in diameter, containing 12 segments of
dsRNA and several proteins (Nuss & Dall, 1990). Of the
proteins, the outer capsid protein is the major constituent
of the virus particles. Therefore, information on the
primary structure of the eapsid protein would be useful
for understanding a major part of the organization of the
particle. The nucleotide sequence of the eighth largest
genome segment ($8) encoding the outer capsid protein
has been analysed for WTV (Xu et al., 1989a) and RDV
(Omura et al., 1989). In WTV, the primary structure of
the P9 protein, which was reported to be another
constituent of the capsid, was studied by nucleotide
sequence analysis of genome segment Sll (Dall et al.,
1989). This paper describes the nucleotide sequence of
genome segment $8 of RGDV which encodes the outer
capsid protein and that of S10 which encodes a protein
with an amino acid sequence highly homologous to the
P9 protein of WTV.
The cDNA library of RGDV genome segments cloned
into pBR322 was described by Koganezawa et al. (1990).
Of the five clones that hybridized specifically with $8
dsRNA labelled with [7-32p]ATP, two corresponding to
the original full-length dsRNA were selected for
sequencing. A series of unidirectionally deleted cDNAs
were formed by digestion from one end with exonuclease
III (Takara Shuzo) and the ssDNAs were prepared for
sequencing. Both polarities of the cDNAs were
sequenced at least twice. Dideoxynucleotide chain
termination reactions and sequence analysis were carried
out as reported by Koganezawa et al. (1990).
The nucleotide sequence of segment $8 is shown in
Fig. 1 (a). The segment contains 1578 bp of dsRNA with
a calculated Mr of 1"01 × l06 and a GC content of 42-5~.
It has one long open reading frame, which starts from
residue 21 and extends for 1278 nucleotides, followed by
a 3' non-coding region of 280 nucleotides. No other open
reading frame, including those in the strand of opposite
polarity, exceeded 54 amino acids.
The open reading frame has the coding potential for a
426 amino acid polypeptide with a calculated Mr of
t Present address: Kobe University, Nada, Kobe 657, Japan.
0001-0297 © 1991 SGM
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2838
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Short communication
47419 (47K). Among the RGDV proteins, the 45K
protein, the major constituent of the outer capsid (Omura
et al., 1985), was the closest in size to the predicted
polypeptide. Hence, partial amino acid sequences of the
outer capsid protein were analysed and compared with
those of the predicted 47K polypeptide. RGDV was
purified as reported previously (Omura et al., 1982).
Amino acid sequencing of the major capsid was carried
out according to the method of Omura et al. (1989). After
electrophoresis of the dissociated proteins of purified
RGDV, the band corresponding to the outer capsid
protein reported as the 45K protein was electroeluted
and digested with trypsin. The peptide fragments were
isolated by HPLC with a reverse-phase column and were
subjected to amino acid sequence analysis using automatic protein sequencers (Applied Biosystems, 477A
and Shimadzu PSQ-1). As shown in Fig. 1 (a), amino acid
sequences of the polypeptide fragments obtained by
digestion with trypsin correlated with the amino acid
residues 85 to 95, 143 to 148, 160 to 166, 363 to 375 and
404 to 407 of the polypeptide predicted from the
nucleotide sequence. These results demonstrate that
genome segment $8 of RGDV encodes the major outer
capsid protein which has previously been called the 45K
protein. The protein is to be renamed the 47K protein.
The phytoreoviruses have almost identical morphologies, based on electron microscopic observation of RDV
(Omura et al., 1989), RGDV (Omura & Inoue, 1985) and
WTV (Streissle & Granados, 1968). They all have
icosahedral double-shelled spherical particles of 65 to
70 nm. The morphological similarity of these viruses is
considered to depend on the spatial conformation of
structural proteins; i.e. the subunit proteins of the
capsomere and the core proteins. The outer capsid of
RDV is composed of 180 capsomeres (Kimura &
Shikata, 1968; Uyeda & Shikata, 1982) which are trimers
of 46K protein subunits (Omura et al., 1989) and the core
of RDV consists of 114K proteins (Kano et al., 1990).
The major outer capsid proteins of the three viruses are
similar in size, 47K in RGDV (Fig.1 a), 46K in RDV
(Omura et al., 1989) and 48K (one of the outer capsid
proteins, P8, encoded by $8) in WTV (Xu et al., 1989a).
As shown in Fig. 1(b), the primary structures of these
proteins show homology: 56, 52 and 48% amino acid
sequence identity between RGDV and WTV, RGDV
and RDV, and RDV and WTV, respectively. Furthermore, approximately 38 % of the sequences are common
among the three viruses. The amino- and carboxyterminal domains of the proteins are especially highly
2839
conserved among the three viruses, i.e. 14 of the first 19
amino-terminal amino acids and 18 of the last 25
carboxy-terminal amino acids are identical in the three
viruses. Some regions with stretches of 10 amino acids
identical were detected between residues 381 and 390 of
RGDV and 377 to 386 of RDV, and between residues
414 to 423 of RGDV and 415 to 424 of WTV. This
similarity in primary structure may result in subunits
being folded to give capsomeres of the same dimensions,
which would make the three viruses indistinguishable in
electron microscopy. The high scores (70 to 75%)
obtained for chemically similar amino acids (Dayhoff et
al., 1972) would also support the supposition that the
spatial conformations of the subunit proteins are
identical.
The similar structures, with homologous arrangement
of the capsid protein amino acids as described above,
nevertheless seem to be serologically distinguishable. No
cross-reaction was observed between RGDV and RDV
(Omura et al., 1985), or between RDV and WTV (Liu &
Black, 1978) when intact virus particles were used as
antigens. The domains with long identical amino acid
sequences are therefore not thought to be on the surface
of the virus particles. This assumption correlates with the
fact that RGDV reacts with antiserum against dissociated RDV particles (Matsuoka et al., 1986). The spatial
disposition of amino acids in capsomeres, and the
interactions between capsomeres and the core should be
discernible by X-ray diffraction studies using crystals of
RDV (Mizuno et al., 1990).
The nucleotide sequence of S10 is shown in Fig. 2(a).
The segment contains 1198 bp of dsRNA with a
calculated Mr of 0-77 x 106 and a GC content of 45-2%.
It has one long open reading frame, which starts from
residue 22 and extends for 960 nucleotides, followed by a
3' non-coding region of 217 nucleotides. None of the
other open reading frames exceeds 61 amino acids.
The open reading frame has the coding potential for a
320 amino acid polypeptide with a calculated Mr of
36095 (36K). High homology was detected between the
36K protein of RGDV and the 38-9K protein of RDV,
encoded by genome segment $9 (Fukumoto et al., 1989),
and the P9 protein of WTV, encoded by genome segment
SI1 (Dall et al., 1989) (Fig. 2b). There is 35%, 32% and
37 % amino acid sequence identity between RGDV and
WTV, RGDV and RDV, and RDV and WTV,
respectively. There are a series of identical six-amino
acid sequences at residues 3 to 8 in the 36K protein of
RGDV and the corresponding region in the 38.9K
Fig. 1. (a) Nucleotidesequence of the plus-sense strand of segment$8 of RGDV and the amino acid sequence of its predicted
translation product. The in-phase termination codon is indicated with an asterisk. The amino acid sequences of several peptide
fragmentswhichhavebeendeterminedare underlined.(b) Alignmentof the predictedaminoacidsequencesof the majoroutercapsid
proteins of RGDV, RDV and WTV, whichare all encodedby genomesegment$8. Identicalaminoacids are boxed. Gaps (-) were
inserted to maximizethe alignment.Numbers are amino acid positions from the N terminus.
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Short communication
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Fig. 2. (a) Nucleotide sequence of the plus-sense strand of segment S l 0 of R G D V and the a m i n o acid sequence of its predicted
translation product. The in-phase termination codon is indicated with an asterisk. (b) Alignment of the predicted amino acid sequences
encoded by genome segment S10 of R G D V , $9 of R D V and S11 of WTV. Identical a m i n o acids are boxed. G a p s (-) were inserted to
maximize the alignment. N u m b e r s are a m i n o acid positions from the N terminus.
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RGDV S10
RGDV $9
RGDV $8
2841
5'
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WTV $9
WTV $I1
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UA
Fig. 3. Comparison ofthe terminal sequence domains ofthe inverted repeats of the corresponding segments (see text)ofRGDV, RDV
and WTV. No segment corresponding to $9 of RGDV and WTV could be detected in segments $3 to $I0 of RDV. Data cited were
reported by Koganezawa et al. (1990) for RGDV $9, Xu et al. (1989a) for WTV $8, Anzola et al. (I 989) for WTV $9, Dall et al. (1989) for
WTV Sll, Omura et al. 0989) for RDV $8 and Fukumoto et al. (1989) for RDV $9.
protein of RDV, and at residues 6 to 11 and 80 to 85 in the
RGDV protein and corresponding regions in the P9
protein of WTV, respectively.
The P9 protein of WTV (Xu et al., 1989b) has been
proposed as one of the capsid proteins (Reddy &
MacLeod, 1976). As mentioned above, the predicted
amino acid sequence of the P9 protein of WTV (Dall et
al., 1989) is homologous to the 36K protein of RGDV
which does not correspond to any protein released from
purified RGDV (Omura et al., 1985). There is no
evidence indicating that the 38.9K protein of RDV is
also a capsid protein.
By including the sequence information for genome
segments $8 and SI0 with $9 of RGDV (Koganezawa et
al., 1990), striking similarities were found in the terminal
structures of the genome segments of all three phytoreoviruses. The terminal sequences, 5" G G . . . G A U Y,
conserved in all the genome segments of WTV (Anzola et
al., 1987), RDV $3 to S10 ( U y e d a e t a l . , 1987, 1989, 1990;
Omura et al., 1988, 1989; Fukumoto et al., 1989;
Nakashima et al., 1990; Suzuki et al., 1990a, b) and
RGDV $9 (Koganezawa et al., 1990), were found in
RGDV $8 and S10. Segment-specific inverted repeats
were also found in residues 5 to 21 and 1557 to 1573 for
$8, and 4 to 16 and 1282 to 1195 for S10 of RGDV (Fig.
3), as reported in all the genome segments of WTV, RDV
and RGDV described above. Thus, the terminal
sequence, 5' G G . . . GAU 3', and the inverted repeat are
structures characteristic of genome segments of phytoreoviruses and may be associated with common
functions.
Terminal nucleotide sequences associated with the
inverted repeat were compared among the three phytoreoviruses (Fig. 3). All nine nucleotides at the 5' and five
nucleotides at the 3' termini were identical among
RGDV $8, $9 and SI0 and WTV $8, $9 and Sll.
However, homology was low between RGDV and RDV,
except for the conserved 5' (GG) and 3' (GAU) termini.
The molecular structures of the genome termini,
assumed to regulate their own expression in WTV (Xu et
al., 1989a), were closer between RGDV and WTV than
between RGDV and RDV, despite the fact that the plant
host and vectors are different for RGDV and WTV and
similar for RGDV and RDV.
The authors are grateful to Dr H. Kano, Dr H. Hirano and Dr T.
Watanabe for their continued interest and valuable suggestions.
References
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Short communication
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(Received 2 April 1991 ; Accepted 10 July 1991)
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