Download Sequence analysis of the 3`-terminal halves of RNA 1 of two strains

Journal of General Virology (1992), 73, 2173-218l. Printed in Great Britain
2173
Sequence analysis of the 3'-terminal halves of RNA 1 of two strains of
barley mild mosaic virus
Satoshi Kashiwazaki, ~.I- Ken Nomura, 1 Hisao Kuroda, 2 Kazutoshi Ito 2 and Hiroyuki Hibino ~
1National Agriculture Research Center, Tsukuba, lbaraki 305 and 2plant Bioengineering Research Laboratories,
Sapporo Breweries Limited, Nitta, Gunma 370-03, Japan
DNA complementary to the Y-terminal halves of R N A
1 of two strains of barley mild mosaic virus (BaMMV)
from Japan, BaMMV-Kal and B a M M V - N a l , was
cloned and sequenced. The sequences start within a
single long open reading frame (ORF), and are
followed by 337 and 338 3' non-coding nucleotides, for
BaMMV-Ka 1 and B a M M V - N a l respectively. The two
strains have 88 % nucleotide identity in the ORFs and
92 % identity in the non-coding regions. The putative
O R F products contain the capsid proteins at the C
termini, as indicated by amino acid sequence analysis,
and two putative non-structural proteins are arranged
in the same manner as in RNA 1 of barley yellow
mosaic virus (BaYMV). The deduced capsid proteins
of BaMMV-Kal and B a M M V - N a l each contain 251
amino acids and have 94 % sequence identity, which is
compatible with their close serological relationship.
Most of the sequence differences between the two
capsid proteins are found in the N-terminal region, and
might explain their serological differences. Significant
sequence similarities of the capsid proteins of the two
BaMMV strains (37 and 35 % respectively) with that of
BaYMV, and their marginal similarities (21 to 26 %) to
the capsid proteins of aphid-borne or mite-borne
potyviruses support the classification of B a M M V and
BaYMV as distinct members of the same virus group,
which is separate from the group(s) containing aphidborne or mite-borne potyviruses.
Introduction
species of Y-polyadenylated ssRNA of 7.6 kb (RNA 1)
and 3.5 to 3-7 kb (RNA 2) (Huth et al., 1984; Ehlers &
Paul, 1986; Usugi et al., 1989; Kashiwazaki et al.,
1989a, b; Anderson et al., 1990).
Hybridization experiments using uncloned or cloned
eDNA and restriction enzyme analysis of cloned cDNA
have indicated that, in either virus, little sequence
homology exists between R N A 1 and R N A 2 (Koenig &
Huth, 1988; Batista et al., 1989; Kashiwazaki et al.,
1989a; Pr61s et al., 1990). It has been shown for BaMMV
that both RNA species are needed for infection (Koenig
& Huth, 1988). BaYMV and BaMMV, however, differ in
some biological and physical properties, and are serologically unrelated (Huth & Adams, 1990). Moreover
hybridization, restriction enzyme and in vitro translation
analyses suggest that their genomes have substantially
different nucleotide sequences (Pr61s et al., 1990).
Examination of the complete nucleotide sequence of the
BaYMV RNAs has revealed close evolutionary relationships between BaYMV and aphid-borne potyviruses
(Kashiwazaki et al., 1989a, 1990a, 1991 ; Davidson et al.,
1991). However the limited similarities in their gene
products, including the capsid proteins, support their
assignment to separate taxonomic groups (Kashiwazaki
et al., 1991 ; Barnett, 1991). No sequence data have been
Yellow mosaic disease causes serious damage to barley
crops in Japan, China and several European countries.
Barley yellow mosaic virus (BaYMV) was first discovered in Japan and has long been implicated as the agent
responsible for this disease (Inouye & Saito, 1975).
However in Europe, another virus, barley mild mosaic
virus (BaMMV), has been shown to be associated with
yellow mosaic disease in combination with BaYMV
(Huth & Adams, 1990). Recent studies also show that
BaMMV occurs in Japan (Kashiwazaki et al., 1990a).
Both BaYMV and BaMMV are transmitted in soil by
the fungus Polymyxa graminis and their plant hosts are
restricted to Hordeum spp. (Huth & Adams, 1990). Their
particles are slightly flexuous filaments with two modal
lengths, 500 to 600 nm and 250 to 300 nm (Inouye &
Saito, 1975; Huth et al., 1984). These particles contain
one species of capsid protein (Mr 31K to 33K) and two
l Present address: Scottish Crop Research Institute, Invergowrie,
Dundee DD2 5DA, U.K.
The nucleotide sequencedata reported in this paper will appear in
the DDBJ, EMBL and GenBank nucleotide databases under the
accession numbers D10949 (BaMMV-Kal) and DI0947 (BaMMVNal).
0001-1056 O 1992SGM
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2174
S. Kashiwazaki and others
BallllV-Kal
13a~i~V-Ka]
UUAU(;G1JU~C1JZACUCAUGUAUC UCGUUUUCUGGGUL~CU@CA~.MACA~;ACGACA
UCACCA~GAO4W~;AMC~A(~AUACAAL~GUGACAA~AU(~GUACGACU
L W L P P }; S C ] S F S (; F L P (; N R T T S P L 1¢ (; K A G I1 T T V T S A W (; T T
120
40
Ba~lilV Kal C~UAC6~6GL~GACGA~G~UC~A~AGAUCAACAAA~AGUUCAA~AC~C~CAGA~U~4GG~C~C~4UAACUC~t~C~AAACAA(~UCGAAAUACC~UCU~AA~L~GAA 240
Ba}tldV Kal
P T R K T K F A T 11 S
BaIIIflV Kal
~MI~V-Kal
UUU{3UUA~CUUCUAUA~UCU~AACCGAUGC(~AACG~GCU~CAA~CCGUGUUCACU~C~'~U{;GAC{~G~GUC~U~C~CA~AL~G~UC~U(~GACAUUC~AUGUCAAU
F V N F Y X L K T l} A N V L {~ ~, V F T A ~1 I) G A V L L Q 2' E X P }~ A O 1 (; 11 V N
Bal~l~V-Kal
BaMMV KaI
AGAC~JGC~J~`~CAG{;ACCAC~UGAAGACAG~GAGA(`~AA~CUG~GCAUGACG~L~CAACACCAU~&~GU~AC~AAC~AUGAAAGAU~;AAGACAGU~GA~UCGACAUGG~ 480
N L L Q 11 I[ F E I) S
T K S
E S
S
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A D L i¢ F S
Q A V 1{ E (;
L N T [
N N S
K P E T S
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80
V K C II L T M K i) G R Q F E L D M E
180
BaM~IV-Kal CAACAC(;AOCCC(;A&4COGUCt;CC&£~.CUUG{;GGC-CGAG(;UUG(;1JUUCAGAA
UGAACA(;AGAC{3ACUUACGUCAAGUU
fA;At~CACACGAUACA~AA~AAGA~AC~CAUCBt~A
Ba~l~V Nal
~
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Ba~I~V-Kal Q II D P E 1' V A K L t; (; E V (; F R M N R D D L ff Q V f; A T I~ Y I N P 1( A Q T S A
Ba}ll~g Nal
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lk]]~]~V-Nal
lk~lll~V Kal
~lll~V-Nal
BaI~I~V Kal
~ t ~ V Nal
~Wl~V Kal
~/tllV-Nal
3B0
120
600
200
~CGA~GCU~I;~(;GC~U(;ACCAUG~.£~C~CAUI;AGt~CUUUCACC~UUG~A~(~AAAGAUG(;~G~AGAAGA~(~£~GA~A~ACUC~U~AU~UUU~CG~GA~UC~ 720
a
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240
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280
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l',a}l]~V Nal
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320
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I~)IMV Kal
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IM~I~V Kal
Ba~II~V Nal
U
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K Y Q V S T S A V C F P I1 Y N N R W G II V [
I~MI~V Kal
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Ba~IIIV Kal
l~a~lI~V Nal
AUC(;UUG(;AAUCCACGUCUCCUACAACGACACGCGCAGAAGAAAlJ(;AGUlJUCAAC~CUUUCACAAGUGACGL~UGACAACGAUUAAUC~AC~CC~ACACGAGAUAC~UUUCA(~AUCG
1200
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l~llI~V-Nal
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L~II~V Nal
(;AI;A~Jl~AA~L`CAGCCAUGClJUCI;UUCCACAGAGUC6UUClJCC~AGUUU~CA~A~ACACA~UAAACUCA~;I;GAA(;U~AAGAAA~ACUCA~ACAAACA~AC~U~ACAGI}A1440
l~lfilV Kal
Ba~IMV Nal
~]~l~V-Kal
l~ll~tV Nal
GAGAAL~;CAUACUUCCUUGAA~CCUGAACACA~CAAACCAUACcAAU(;GGU~AGIL~CAU(~;ACGA(;UAC~ALL~UC~AUCC~UUAUGACC~GUAU~UC~(;A~UGAAG1560
C U
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g S P Y F L E F L S 'r F K P Y Q W V Q A F }~ l) IS Y A P S I L A Y D A Y F K D L K
520
Ba~I~V-Kal
I~l~l~V-Nal
l~lll~V Kal
Ba]dl~V Nal
AAAUAUGAUAG(g~CACEACACGCA~AUGUUL~CUGUC~GGA~A~BA~L~2AAAE4~UA&h~AUAAGAUGAUCA~AU~GA~AA~A~AU~S~(~;AC~UAGUACGAAL~AL~ Ifi80
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l~tl~V Kal
M~l~V Nal
~llllV Kal
GAI;~AGGUCUUGCUUGACAUC1;CI;~JG{;ACCACCUCCGGUGGACCCL~UGUACCAU~;UAAGA~AUCGA~AL~GU~AACAC~UG~I~ACG~C~A~UUGUACA~UUCAGU~A~U(~ 1800
l~l~V Kal
I!allllV-Nal
MllllV-Kal
I~IIIIV Nal
~A~AGGCU~UUAUCA~UGGAA~GCU~;I;MJGG~UCUGGAA~AUC~CUCAAA(;CCGA(;CU~(;CU~UU~(~A~£~AAU~U~IGAAAA~G~U~A~UC~U~L~AUA
C
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~llltV Kal
Ba~llIV Nal
P,a]iilV Kal
I~]IItV-Nal
A~AAGCCU~AUUI`'CGAUGAAAU~UAUI;UC~GAUG~UUU~AA~AG~U~UAA~A~A~U~A~AC~(~A~A~AGUCC~AU~AA~A~GU~AA~G~U~AGAAU~UG 2040
~ItlIV Kal
Ba}t~V-Nal
L~tI~V Kal
Ba)i~V Nal
(; C A U
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Ba~IMV-Kal AC(G
; AACA~ACAAAG~AC~]CG~CACAAUCUACGAAGMA
; UAGUCAACACGAAGAUAUGUCUGC~GAACGGCCUC~UC~CAGAA(~
;A~`~GGAAC~C~GUC~C~AC~CAA(~ACU
0C {; [
II K E L P T
{; A
T EII
A
Ba~I~V-Kal
Balll~V Nal
lkal~llV Kal
lk~ll~V Nal
~;UUGU~G~CAACACACUCI~ACUCAUGAC~C¢JUUUUCUEUACGCAU~U(;CL~I;(x2l~CA~UGGAGAUCAC~UU~GAACUCAU(~AC~;A~ACUUC6UCUUCGUCU(EAAUG~U~AUGAC
2400
{2 C
U[
U U
C
A
{; A
U
U
C C C
V V O N T L A L M T A F L Y A Y A R L T G D II A F E L t~ O E N F V F V C N (; D O
80(}
S
P T
K I
UA A U U A
C A
U A
U C A
(;
C L A N (; L V I q K N C {; N N S 6 Q P S
228B
Ba~[IV-Nal
M~IMV-Kal
Baill~V Nal
l
U
A P U
Y E E I V N T
72B
T
760
lk~}~l~g-Kal AAC~A~UUUUCC~UGUC~CCU~GC~JU~UGGC{;A~{;UUUG{;AU{;C~AUUUCU~CCC~UUCCU~U~U~;~;CUC~{~UAA~UACGA~U~UGM{~CUGA~6AUAUCU{~G~AA~2520
BalllV-Nal
C{;
C
U
C (;
U
A
(; C C
C C
C
U
Ba}~}~V Kal N K F S }fl S P S F ~ A K F (; C 1) F S P F L S E L {; L T Y E F 1) E A T G 1) I C E N
840
I~}~I~V-Nal
A_
V
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2175
Nucleotide sequence o f B a M M V R N A 1
BallldV Kal CCCUACA~GUCCUUGACGAUC4;UCCGCACCUCGUUUGGGAUUGGUUUCUCUCUCUCC~UUGAGC~A~C~AGU~;~G~GGUC~AGU~UC£AU(~CUA~ 2640
I~MMV Nal
C
U
C
C C
C A
C
A
C U U
BalMV-Kal P Y M S L T M V R T S F (; 1 G F S L S I E R I V A 1 L Q W S l~ A (; G V L II A Y L
880
BaMMV Nal
BaMMV-Kol ~C~3C~GCCGCUCUULqJ(~;A~UCUUUCAACACACCCA~AC~UIjC~UCUCGU(?~ACAC~U~UCUCCUUUGGCUCG~AC~(~ACGAGGA~;A~CUC~UCCAUGAU~C~2760
Bal~MV Nal
U
(; C
C
C
C
~.
G
~J
~J U G
Ba~I~V Kal S (; I A A L F E S F N T P K L F N L '/ ]1 T Y L L W L V T E If E E E L V S M J8 E L
920
I~IMMVNal
I~MV Kal AAAGACAUGU~£AUGCCCUUGCCCACUAGGGAACAGAUAGCCUU~CUGCACUACG~.~UGGAACUGAGCCCAUCG~GGAGGAAACA~U~AA(~A(;~;ACAC~;AAGA~A(;A~
2880
Ball~V-Nal
G U
UC
A
U
A C
A
A
A
U
AA U U
U
U
BalAMVKal K P ld F i~ P L P T I~ E (~ I A L L ]I Y V t; T E P I V E E T F L QZA (; II E E P I) P I
960
I~-~MI~VNal
K
M
Y
| S"
K P
D
I~MMV Kal ~;UUCCCCCAG~J~J~UGACACCY;AUCU~A~(;&AC~UC'(~U(L`C(~&CC~(X)C(;AC&~AG/~JL~`~;UC(;C(~G~A~GU~;A~KG~CU~C~UG~CL~AUG 301}0
BalIMV-Nal
U
U
U
c A
A
(;
(;
AUU
(;
I~I~MV Kal ~ P P V P 1) T 1) L T N 1~ A A A P P O N 1~ K S R A V 1 P R G T S D W S L P E P K ]~
lOOO
~lIMV-Nal •
S
I~
V
N
BaMIdV Kal CGAACACUG(~UUUC/~(;UCCAAGAUCAACAUCGAAACACUIJ~;~x2AAUGUCC~CGACG(~UAUAUGAACACCUUUCd2~R2CGUUGCAACU(;AA~C(~AA~UA~AU~;A~AG(~
312(I
I~MMV Nal
UG A
A
A
(; C (;
A
U
i;
A
A
Ba~llflVKal l~ T L (; F K S K I N 1 E T L A N V P D (; Y M N T F A S V A T E S O R I~ K W E E A
1040
BaMI~VNal
M
1)
E
T
BaHMV Kal
~a2ACGUG(~(;AUUUC~;~AU~ACU(;ACGAUGAGA~AUG(;(;AGAA~UUGCUcAUUG~Uf7~l~GUAUAUAUUUC~A(;AC~UG~A~A~(;~;ACGA~AACUCA~UAUGGA~
3240
~MHV Nal
A (;
U
U
l~]dV Kal A I¢ (; 1) F (; I
Ba}~MV-Nal T
C
AC
(;
A
C
T 1) l) E K W E K b L I
N
C C
A A C I
U
A C
U
t;
A
Y F A O N (; T S P N F O E E L T M E
lhtflflV Kal (;UUAA~(;(;C(;(;UCU~CCAU~A/~AG~(;UA~CCC(;UUCGCCCCUUU(;~`(;UU~GA(~A~AU~C~U(~A~UCU~(~U~U~A~A~UCAU~
I~MM¥ Nal
C
U
C
U
O C (;
C
A
~;
U (;
h A
[~MMV KaI V R (; (; L N S I K ~ Y P V R P F ¥ ¥ R A IK K I S "r L I~ 1~ I F 1~ C Y S I ~ T K L ~l
l~l~lflV Nal
1080
3360
I120
BaMMVKal UU~(~GAAGCUGAGGC~7~GUG~CACACU~;G(;~C~UAAA(;~AC~;GAU(;CCU~GAUGAG~GUC~UG~U~CAU~AUC~GA~AGU~ACCUCUA(;(;ACU~(~UU(;~CACUGAAG
3480
BaMMV--Nal
A
A
U
(;
U
A
C
A
U C A
A C
BaMMV Kal F V K L 1~ R V P 11 W A I K II {; C L O E l V F 1) F lfi I P O Q F T S 1{ T A L E 'f L K
1160
I~MMV-Nal
Q
BaI~MVKal
~MI~V Nal
~BI~V Kal
~lflflv Nal
CAGACCAAACU(;~JUGC~AUUGGUGUU~(~CACAA(~CAAUUCUCUCCUCACCUC~;~(~AGAC~;AACAU~A(~;A~ACU~AC~GAC~A~(~U(;ACUACGA~(~;UCA~;A~UC
3600
(; U
A
A
A
C
C
U
Q T ~ L A /~ I (; V l; 'r S N S L L "r S E (~ 'I N I~ t~ 7 7 E '1' R R 1~ N D '/ O (; II E A L
1200
BaMMVKal ~UcCGG~A~A~U~UC~GCA~UGC~UUUCCUUUUAAGCAAU6C~U~UCAA~AcGCUUUUAAUUAUAUCAA{~GU~AAGMU~cUc~UU~A~;~U~A~
;GUW~AcU 3720
Ik~MMV-Nal
(; A
CA (; C
C
A C
LE
C
(; (;U
(;
Ba~MV Kal L 1¢ *
BaMMV-Nal
l',ai~MV Kal
I ~ V Nal
UUGUG~AUGCAAU(~GAAAAUIJCAGUGAC(;CAAUCAACCAUCAUUC4;UU~;UGACA.ACGCAGUACU~OUC~qJ
AUUUCACAUCAAGCi;ACCA(;CACAUC(~-.JJCC,
CUUACAGCUAAUCCUA 3840
C (;
h
C UG
CO
U
I~MMV Kal
I~MMVNal
C~UGAG(;(;U(;GC~CUCU~;UGUUAUGUA~U(~AAUGU(;CA~UCUCGCAALE~CCGUC~U~J(~;UUGAUG(;U(~G(~AACA~C(~C~C~G~AUACC(~A(~(A)n
A
A
C
Fig. I. T h e n u c l e o t i d e s e q u e n c e s a n d d e d u c e d a m i n o acid s e q u e n c e s of the Y - t e r m i n a l 3946 n u c l e o t i d e s from B a M M V - K a l R N A 1 a n d
o f the T - t e r m i n a l 3464 n u c l e o t i d e s f r o m B a M M V - N a l R N A 1. T h e B a M M V - K a l s e q u e n c e is g i v e n in its entirety, w i t h o n l y the
differences from B a M M V - K a l b e i n g g i v e n for the B a M M V - N a l sequence. # i n d i c a t e s the start of the B a M M V - N a l sequence.
Possible c l e a v a g e sites for p o l y p r o t e i n p r o c e s s i n g are s h o w n by arrows. A possible p o l y a d e n y l a t i o n s i g n a l ( U A U G U ) is underlined. T h e
N - t e r m i n a l a m i n o acid s e q u e n c e s d e t e r m i n e d by d i r e c t protein s e q u e n c i n g for the B a M M V - K a l a n d B a M M V - N a l c a p s i d p r o t e i n s are
boxed.
published for the RNAs of BaMMV. lmmunoelectron
microscopic tests failed to detect any serological relationship between BaMMV and BaYMV, although relationships were found between BaMMV and aphid-borne
potyviruses (Stanarius et al., 1989). It is therefore of great
interest to compare the capsid protein amino acid
sequence similarities between BaMMV and aphid-borne
potyviruses or BaYMV.
Although the use of resistant barley cultivars is the
only practical means to avoid damage caused by yellow
mosaic disease, resistance-breaking virus isolates have
been reported in Japan, Germany and France (Kashiwazaki et al., 1989 b, 1990 b; Friedt et al., 1990; Hariri et al.,
1990; Huth, 1990). For example, Kashiwazaki et al.
(1990b) described two Japanese BaMMV strains,
BaMMV-Kal and BaMMV-Nal, which infect barley
cultivars having the BaYMV resistance gene Y m l , but
differ both in pathogenicity towards different barley
cultivars and serologically.
Here we report the nucleotide sequences of the 3'terminal halves (which include the capsid protein gene)
of RNA 1 of BaMMV-Kal and BaMMV-Nal, and we
assess similarities at the nucleotide and amino acid levels
among these BaMMV strains, BaYMV, and aphid-borne
or mite-borne potyviruses.
Methods
Virus purification and R N A extraction. T w o B a M M V strains,
B a M M V - K a l a n d B a M M V - N a l , were p r o p a g a t e d in barley by
m e c h a n i c a l i n o c u l a t i o n a n d t h e i r p a r t i c l e s were purified as d e s c r i b e d
by U s u g i & Saito (1976). V i r a l R N A w a s isolated f r o m purified v i r u s
p a r t i c l e s as d e s c r i b e d by K a s h i w a z a k i et al. (1989a).
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S. Kashiwazaki and others
cDNA cloning. Double-stranded cDNA was obtained from a mixture
of RNA 1 and RNA 2 as described previously (Kashiwazaki et al.,
1989a). The cDNA product of BaMMV-Kal was size-selected ( >
approx. 3 kb) by 1% low melting point agarose gel electrophoresis and
then ligated into SmaI-cut, dephosphorylated pBluescript II SK(+).
The cDNA product of BaMMV-Nal was ligated to an EcoRI NotIBamHI adaptor (Takara Shuzo) and then size-selected ( > approx.
3 kb) electrophoretically. The cDNA with the adaptor was phosphorylated by T4 polynucleotide kinase and ligated into EcoRI-cut,
dephosphorylated pBluescript II SK(+). The cDNAs were used to
transform competent NM522 cells.
Screening ofcDNA clones. Colony hybridization was done using viral
RNA 1 and RNA 2 probes isolated electrophoretically as described
previously (Kashiwazaki et al., 1989a) and the ECL gene detection
system (Amersham). Two large cDNA clones, KalSK11 (4 kb) and
KalSK46 (4 kb) derived from BaMMV-Kal RNA 1, and two other
clones, NalSK2 (3.5 kb) and NalSK15(3.5 kb) derived from BaMMVNal RNA 1, were selected for sequence analysis.
DNA sequencing. A series of unidirectionally deleted cDNAs were
produced by digestion from one end of a clone by exonuclease III and
the ssDNAs were prepared for sequencing. The nucleotide sequences
were determined by the dideoxynucleotide chain termination reaction
(Sanger et al., 1977) using an automated DNA sequencer (377A,
Applied Biosystems) as described previously (Kashiwazaki et al.,
1990a).
Protein sequencing. Capsid proteins from dissociated virus particles
(approx. 15 ~tg)of BaMMV-Kal and BaMMV-Nal were separated by
SDS-PAGE (Laemmli, 1970), and then blotted onto the Problot
membrane (Applied Biosystems) in 10 mM-3-cyclohexylaminopropanesulphonic acid (pH 1 I) and 10% (v/v) methanol using the Mini-Transblot Electrophoretic Transfer Cell (Bio-Rad). The blots were stained
with Coomassie blue R, and the capsid protein bands were excised.
Amino acid sequences were analysed in a gas-phase protein sequencer
(477A, Applied Biosystems).
Computer analysis. Sequence data were compiled and analysed using
DNASIS (Hitachi Software Engineering) or U W G C G (Devereux et
al., 1984) software packages.
Amino acid number
500
1000
(a)
.
.
.
.
.
I
.
.
.
.
/"
//
/
2000
/
/
/
1000
/
[
,
,
,
i
BaMMV-Kal
500
1000
(b)
3000
/
J
/
>
/
/
2500
/
/
2000
f
r
f
f
I
,
,
,
,
BaMMV-Kal
150O
(c)
I
20O0
.
.
.
.
I
3000
,/
/
>
e~
(
/
2500
/
Results
Clones KalSK11 and KalSK46 covered the T-terminal
half of BaMMV-Kal RNA 1 in opposite orientations.
Clones Nal SK2 and Nal SK 15 covered the corresponding region of BaMMV-Nal RNA 1 in the same manner.
Sequence analysis of KalSK11 provided the T-terminal
3946 nucleotides, upstream of the poly(A) tail, of
BaMMV-Kal RNA 1 in the 5' to 3' direction and these
sequences were confirmed by the sequence obtained for
KalSK46 in the reverse orientation. The Y-terminal
3464 nucleotides of BaMMV-Nal RNA 1 were sequenced using NalSK15 in the 3' to 5' direction and were
then confirmed using Nal SK2 in the reverse orientation.
The nucleotide sequences obtained are shown in Fig.
1. Both sequences start within a long open reading frame
(ORF) which terminates with an UAG codon at position
3607, leaving 337 non-coding nucleotides for BaMMVKal and 338 for BaMMV Nal at the 3' terminus. These
non-coding regions have 92% nucleotide sequence
2000
BaYMV
Fig. 2. Dot plot comparisons of the partial polyproteins encoded by
BaMMV-Kal RNA 1 and BaYMV RNA I (a), BaMMV-Kal RNA 1
and PVY RNA (b), and BaYMV RNA 1 and PVY RNA (c). Data were
analysed using the U W G C G program DOT with a window of 21 and a
matching number of 14.
identity with only one gap in the middle (at position
3793). As observed with the BaYMV RNAs (Kashiwazaki et al., 1989a, 1991), a possible polyadenylation
signal (UAUGU; Zaret & Sherman, 1982) was found 85
nucleotides upstream of the poly(A) tail.
The partial ORFs found in BaMMV-Kal and
BaMMV-Nal RNA 1 encode large polypeptides of 1202
and 1041 amino acids, respectively. The sequences of the
two ORFs were aligned without a gap, showing 88%
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Nucleotide sequence of B a M M V RNA 1
identity at the nucleotide level and 96~o identity at the
a m i n o acid level. Direct sequencing o f the capsid
proteins gave their N-terminal sequences, A G H E E P D P I V for B a M M V - K a l
and S G K D D P D P I V
for
B a M M V - N a l , both of w h i c h are located in the putative
O R F products at positions 952 to 961. T h e predicted
capsid proteins o f the two B a M M V strains each contain
251 a m i n o acids, with calculated Mr values o f 28421 for
B a M M V - K a l and 28510 for B a M M V - N a l .
D o t plot comparisons (Fig. 2a) showed that the O R F
products share extensive homologies with the C-terminal
half o f the 270K polyprotein encoded by B a Y M V R N A 1
(Kashiwazaki et al., 1990a). Thus by analogy with
B a Y M V , the O R F products o f the two B a M M V strains
start within the N I a region, followed by the N I b and
capsid protein regions (Kashiwazaki et al., 1990a). T h e
N I b and capsid protein regions found in the B a M M V
polyproteins are separated by respectively Q A (in
B a M M V - K a l ) or QS (in B a M M V - N a l ) dipeptides
which correspond to the Q A dipeptide at the equivalent
position in the B a Y M V polyprotein (Kashiwazaki et al.,
1990a). The QS dipeptide found in both B a M M V strains
at position 417 corresponds to the Q A dipeptide at the
putative b o u n d a r y between the B a Y M V N I a and N I b
regions (Kashiwazaki et al., 1990a). D o t plot comparisons of the B a M M V O R F products and the potato virus
Y (PVY) polyprotein (Robaglia et al., 1989) displayed
significant but limited similarities in each region (Fig.
2b). These similarities were o f the same extent as
those found between the B a Y M V and P V Y polyproteins
(Fig. 2c).
Table 1 presents the percentage of identical a m i n o
acids found in the alignment of three protein regions
from B a M M V - K a l , B a M M V - N a l , B a Y M V , six aphid-
Table 1. Percentage of identical amino acids* found in three regions from viral polyproteins
(a) Capsid protein region
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
PPV
TEV
TVMV
BYMV
TuMV
WSMV
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
PPV
TEV
TVMV
BYMV
TuMV
94.0
37.2
24.9
25-0
24.6
23-2
23.6
26-3
24-2
35.2
24.2
23.3
25.4
22.4
21.4
25-8
24.1
24.5
22.7
25.3
26.5
20.1
23.2
20.3
58.9
62.7
53-6
61.1
62.9
25-8
60.1
49.8
57-5
59-7
26-4
57.8
64.3
62.8
26.6
58.2
52.5
25-8
51.1
26-9
25.7
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
PPV
TEV
96.6
57-7
33-2
32-9
34.7
32.3
57.9
33.0
34.1
35.3
33.1
32.8
33.3
35-2
31.8
62.2
58.5
61.4
62.7
61.0
62.5
BaMMV-Kalt
BaMMV-Nal t
BaYMV
PVY
PPV
TEV
96.9
31.7
20.9
22.3
18.9
20.8
37.8
22.6
23.0
20.0
20.5
19.9
20.4
19.8
20.8
54.0
48.1
46.4
51.6
50.5
48.8
(b) Nlb region
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
PPV
TEV
TVMV
(c) NIa region
BaMMV-Kalt
BaMMV-Nalt
BaYMV
PVY
PPV
TEV
TVMV
2177
* Percentage identity was calculated with the UWGCG program GAP which made an optimal alignment of two sequences.
t Only partial sequences were available for comparison.
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2178
S. Kashiwazaki and others
(a)
BaYMV
PVY
TEV
TuMV
BYMV
PPV
TVMV
WSMV
AADPLTDAQKEDARIAAADGARFELADADRRRKVEADRVEAARVK
ANDTIDA
GGTV
AGETLDADLTEEQKQAEKEKKEREKAEK
SDQEQLNAGEEKKD
ADEREDEEEVDAGKPIVVTAPAATSPILQPPPVIQPAPRTTAPMLN~IFTPATTQPATKPVSQVPGPQLQ
SDTVD
QSNNVSVMAGLDTGGAKTG
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
TEV
TuMV
BYMV
PPV
TVMV
WSMV
DASADVGKKKDQKD~KVAEQASKDRDV~AGTSGT~PRMKGEVVV~LNH~LGYKPQQ
ERERQKQLAFKKGK~VAQEEGKRDKE~GTSGT~PRYEKRVAL~LDH~ILYTPEQ
BaMMV-Kal
BaMMV-Nal
BaYMV
PVY
TEV
TuMV
BYMV
PPV
TVMV
WSMV
BaMMV Kal
BaMMV-Nal
BaYMV
PVY
TEV
TuMV
BYMV
PPV
TVMV
WSMV
BaMMV-Kal
BaMMV Nal
BaYMV
PVY
TEV
TuMV
BYMV
PPV
TVMV
WSMV
TFGTYGNEDAS~SNSNA~V~TNRDRDVDAG~IGT~KLSLPKVKG~AIF~LNH~YSPAQ
~KDKARDQKLADKP~LAIDRTKDKDV~TGTSGT~MNM~LPKV~GS~VV~LD}~LTYKPAQ
Q~SGSKGTGGSFTSNPVR~GGR~TDVQDQTPGLM~TVRDKI~PEM~NNMIKYQPRT
.
•
~E~N.MP~VM~LNV~CIE
~NVgTA~N~EEQ.SKZ~aFMVWC~
~LS~S~~F~V~Y~L~.MQZ~N~LaV~CIE
D D I S N V I ~ Q E ~ F E A ~ Y N G V K Q A Y E V E ~ S R . MGI I~NGLMVWCIE
VDLSNTR~_PQ~CFQT~Y~GVKR~YD~.MSII~NGLMVWCIE
EFVVNTR~J}~FKA~HTNVMAELELNEEQ.MKIV~/~NGF~WCIE
ELIDNRY~T~NT~IKE~SEGLDV~E~VFINT~PGWVYHCII
.
.
.
~ W g V
.......
NNMM~C~I~
~ g~ g~ L~ G T . . . . . . .
NNMMDeDE
~ e ~
.......
~SDe~D
~LQG~
. . . . . . . W~MD~EE
~ M ' ' I
..... W~MMDGET
~ 9 ~ I S G V . . ' ..... WTMMDGDE
~NRALG~WRVVNNAGKDNEQ
~ g ~ K E P Y M P R Y G N I R N L R D V G L A R Y ~ Y E V T
I EMRN~. ERPYMPRYG~QRN ITDMSLSRY ~ Y E L T
• ~~AYIE~NQ.DRPYMPRYG~QRNLTDMSLARY~YEMT
P~F~MSHF~FVAEAYIE~NA.TERYMPRYE~QRNLTDYGLARYA~95{~YELT
P~F~VARF~VAEACVE~NY.EKAyMPRYG!QRNLTDYSLARYA~YEMT
P~S~~NRNS.EQVY~PRYGNQRGLVDRNLAPFA~FEVN
~~EESV~IGKPI~PR~DFKAGVLSINNIVAAC~IMRG
QQVS~/I~LT~: " P~F~MTHF~DLAEAY
QL~FKI~YKA~.
~ E N ~ E ~ H T
~ T A E E D ~ H
~ T T V E N ~ H
~ G T D E E N ~
~ V G T Q K Q I
~ ~ H ~ y N
ADDTPNFVQVQNSVA
T < ~ V S P S M H T L L G V K N M
T A H ~ V N R N M H T L L G V R Q
T T E ~ V I R N M H N L L G V Q G L
H T A G ~ Y N R D M H T M L G V R I
~ H T ~ V N R N M H T F L G V R G V
A Q M H H L L G V K G V
VR~NTHSFNGVNALA
(b)
BaMMV-Ka I
BaMMV-Na I
BaYMV
PVY
PPV
TEV
TVMV
PD~TIVF,~FR . . . .
PI~IVK~F
,
PIf6~TImK~H
,
P
D
~
T
~
BaMMV-Kal
BaMMV Nal
BaYMV
PVY
PPV
TEV
TVMV
G ~ Y ~ V ~ H ~ L F ' g ~ I L ~ K D F P V F P Q K L H . . . F
G F ~ L ~ V T N Q ~ L F ~ I ~ L ' ~ K D F P P F P R R L Q . . . F
G F ~ P F ~ ] T N K ~ L F ~ ~ D F P P F ~ K L K . . .
F
GF~PY~NQ~LFRRNN
MAKDFPPFPQKLK...F
BaMMV-Kal
BaMMV Nal
BaYMV
PVY
PPV
TEV
TVMV
R~JQNERIC.~VGTNFQENYA~~F~N~LP~C]VSTADGC~SLA
R ~ T E D R V C ~ I G S N P Q ~ S I ~ ~ L P I V S T R D G S ~ S L A
R ~ R E E R I ~ V T T N F ~ S M ~ ~ P L V S T R D ~ S A S
R Q ~ I K D R V C M V S T N F Q ~ S V ~ ~ S P L V S I I D G N ~ S L T
•
S
A
S~MVV~LIKECVE..~[EINSTC~F~LLIAVN~EKES
VIL~T~SLLK~GHH..P~DTH~CICRYFV~LVLAVH~AYES
~ MVII~TCEK..CG..INKEEIV..YYV~LLIAIH~DKAE
MVVL~M~LSK~GV~..INSQEDVCK~FA~LIIAI~ELEH
illll
Fig. 3. Alignment of amino acid sequences of the capsid (a), NIb (b) and NIa (c) proteins of BaMMV-Kal and BaMMV-Nal with the
corresponding proteins of BaYMV, PVY, PPV, TEV, TVMV, TuMV, BYMV and WSMV. The capsid protein sequences are shown in
their entirety. The partial NIb region (at positions 731 to 811 in Fig. 1) and NIa region (at positions 236 to 368) of BaMMV-Kal are
aligned with the equivalent regions of other viruses. Amino acids identical to the BaMMV-Kal sequences are boxed. Amino acids of
specific motifs are indicated by asterisks (see text).
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Nucleotide sequence o f B a M M V
borne potyviruses [PVY, plum pox virus (PPV; Maiss et
al., 1989), tobacco etch virus (TEV; Allison et al., 1986),
tobacco vein mottling virus (TVMV; Domier et al.,
1986), bean yellow mosaic virus (BYMV; Hammond &
Hammond, 1989) and turnip mosaic virus (TuMV;
Tremblay et al., 1990)], and a mite-borne potyvirus
[wheat streak mosaic virus (WSMV; Niblett et al.,
1991)]. Amino acid sequences of the ORF products of the
two BaMMV strains are highly conserved but the
similarities between the two BaMMV strains and
BaYMV are much lower in all three regions. Amino acid
sequence comparisons between BaMMV and aphidborne or mite-borne potyviruses and between BaYMV
and these viruses reveal only a low level of identity in all
the regions examined. The sequences in the NIb regions
are more conserved between BaMMV or BaYMV and
the potyviruses than those in the NIa or capsid protein
regions.
Amino acid sequence alignment of the capsid proteins
of BaMMV-Kal and BaMMV-Nal (Fig. 3a) shows that
their N-terminal regions are more variable than the
remainder of the sequences; four of the first five amino
acids differ between the two strains. The two conserved
blocks NGTS and AFDF found in the core regions of the
BaYMV and potyvirus capsid proteins (Kashiwazaki et
al., 1989a) are also present in the corresponding regions
of the two BaMMV strains at positions 1067 to 1070 and
1141 to 1144 with a replacement of the A by V in the
second block. Alignment of the BaMMV and BaYMV
capsid protein sequences also shows many differences in
their N-terminal regions in contrast to extensive homologies in their core and C-terminal regions. In the core
regions of the capsid proteins, only limited similarities
exist between either BaMMV or BaYMV and aphidborne or mite-borne potyviruses.
The two conserved stretches (T/S)GXXXTXXXN(T/S) and GDD, thought to form the core of RNAdependent RNA polymerases of positive-strand R N A
viruses (Kamer & Argos, 1984; Domier et al., 1987),
are present in the NIb regions of BaMMV-Kal and
BaMMV-Nal at positions 755 to 765 and 798 to 800
(Fig. 3b), as found also in BaYMV and aphid-borne
potyviruses (Kashiwazaki et al., 1990a; Koonin, 1991).
The triad of catalytic H, D/E and C/S residues found
for cysteine proteinases of comoviruses, nepoviruses,
aphid-borne potyviruses and BaYMV (Gorbalenya et al.,
1989a; Dougherty et al., 1989; Kashiwazaki et al.,
1990a) are also present in the NIa regions of the two
BaMMV strains at positions 246, 282 and 349 (Fig. 3c).
Discussion
This study suggests that the T-terminal half of BaMMV
RNA 1 is translated into the C-terminal part of a
RNA
1
2179
polyprotein from which the NIa, NIb and capsid
proteins are derived by proteolytic cleavage in a manner
similar to that for the translation products of BaYMV
RNA 1 (Kashiwazaki et al., 1989a, 1990a) and aphidborne potyvirus R N A (Dougherty & Carrington, 1988).
As established for aphid-borne potyviruses (Dougherty
& Carrington, 1988; Riechmann et al., 1992), the
putative NIa proteinase found in BaMMV would be
responsible for the proteolytic activity. The putative
cleavage site between BaMMV NIb and capsid proteins
is QA or QS, compared with QA, QS, QG or QV in
BaYMV and aphid-borne or mite-borne potyviruses
(Shukla et al., 1991). The QS dipeptide found between
the BaMMV NIa and NIb regions is probably the
cleavage site because of its position, although comparisons of the amino acids surrounding this dipeptide with
those at the site between the NIb and capsid proteins
show no identical amino acids or significant chemical
similarities.
Analysis of peptides released by mild proteolysis from
the aphid-borne potyvirus and BaYMV particles has
demonstrated that the N- and C-terminal regions of their
capsid proteins are located on the surface of the virus
particles (Shukla et al., 1988; Kashiwazaki et al.,
1989 a). The degradation observed in the BaMMV capsid
protein (Ehlers & Paul, 1986; Kashiwazaki et al., 1989b)
as well as the relatively hydrophilic nature of the
terminal regions of the BaMMV capsid protein sequence
(data not shown) may also indicate the surface location of
the terminal regions. It has been shown for aphid-borne
potyviruses that the long surface-located N-terminal
region of the capsid protein is the immunodominant part
of the protein and is so variable among viruses that it
contains virus-specific epitopes (Shukla et al., 1988,
1989). The large amino acid sequence differences
between BaYMV and BaMMV in the N-terminal
regions of their capsid proteins fit well with the absence
of serological relationship between them. The difference
observed in the stabilities of their capsid proteins (Ehlers
& Paul, 1986; Kashiwazaki et al., 1989b) may be
attributable to differences in the occurrence of cleavage
sites for the protease(s) that probably contaminate
purified virus preparations (Ehlers & Paul, 1986). The
extent of the capsid protein sequence similarities
between BaYMV and the two BaMMV strains (35 or
37%) is comparable to the lowest value among the
identities reported for distinct aphid-borne potyviruses
(38 to 71%) (Shukla & Ward, 1988). Relationships
between BaMMV or BaYMV and aphid-borne potyviruses are even more distant. Thus, although Stanarius et
al. (1989) reported that BaMMV reacted with antisera to
the aphid-borne potyviruses BYMV and TuMV, it has
only slight capsid protein sequence similarities (21 to
26%) with these two and other aphid-borne or mite-
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2180
S. Kashiwazaki and others
borne potyviruses. Likewise, the BaYMV capsid protein
has only weak similarity (20 to 27~) with those of
aphid-borne or mite-borne potyviruses. Furthermore,
the (I/V)DAG sequence implicated in aphid transmission of potyviruses (Harrison & Robinson, 1988; Atreya
et al., 1990, 1991) is not present in the N-terminal regions
of the capsid proteins of BaMMV or BaYMV, which are
fungus-borne. The sequences of the non-structural
proteins of BaMMV and BaYMV also slightly resemble
those for aphid-borne or mite-borne potyviruses. These
results support the current proposal that BaMMV and
BaYMV should be distinct members of the genus
Baymovirus, which is placed together with the genera
Potyvirus (aphid-borne) and Ryemovirus (mite-borne) in
the family Potyviridae (Barnett, 1991).
The considerable similarities between BaMMV-Kal
and BaMMV-Nal, in their capsid and non-structural
protein sequences and in their 3' non-coding nucleotide
sequences, are comparable to those reported for strains
of individual aphid-borne potyviruses (Shukla & Ward,
1988; Ward & Shukla, 1991). This supports the classification of BaMMV-Kal and BaMMV-Nal as strains
of the same virus (Kashiwazaki et aL, 1990b). The
several amino acid differences found between the Nterminal regions of their capsid protein sequences could
cause their serological differences (Kashiwazaki et al.,
1990b), suggesting the presence of strain-specific epitopes in this region. However, because polyclonal
antibodies raised against the two BaMMV strains are
cross-reactive (Kashiwazaki et al., 1990b), monoclonal
antibodies seem to be required for virus strain identification. Alternatively, it would seem possible to identify the
two strains by hybridization techniques using oligonucleotide probes for strain-specific blocks of nucleotide
sequence. The relation between sequence differences
between the two strains and their differences in
biological properties, such as pathogenicity, remains to
be determined.
The authors wish to thank Professor B. D. Harrison, University of
Dundee, for critical reading of the manuscript.
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BARNETI, O. W. (1991). Potyviridae, a proposed family of plant viruses.
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